
============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 128}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

  Time building chain proxies: 1.19, per 1000 atoms: 0.54
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.654, 64.232, 43.217, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A VAL  112": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU  132": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.045, 62.92, 68.419, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A ASP  110": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.96, per 1000 atoms: 0.43
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.403, 56.226, 64.502, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.996, 38.703, 43.032, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

  Time building chain proxies: 0.97, per 1000 atoms: 0.44
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (43.447, 53.876, 42.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  ILE A  78 "
        model="   7" pdb=" CB  LYS A  79 "
        model="   7" pdb=" CB  TYR A  89 "
        model="   7" pdb=" CB  ILE A 122 "
        model="   7" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 0.91 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 56
        1.23 -     1.43: 419
        1.43 -     1.62: 652
        1.62 -     1.82: 9
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" N   MET A 128 "
       model="   7" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.725 -0.267 1.90e-02 2.77e+03 1.98e+02
  bond model="   7" pdb=" N   ARG A 127 "
       model="   7" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.636 -0.178 1.90e-02 2.77e+03 8.76e+01
  bond model="   7" pdb=" N   SER A 130 "
       model="   7" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.620 -0.162 1.90e-02 2.77e+03 7.31e+01
  bond model="   7" pdb=" N   VAL A 126 "
       model="   7" pdb=" CA  VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.599 -0.141 1.90e-02 2.77e+03 5.51e+01
  bond model="   7" pdb=" CA  GLY A 121 "
       model="   7" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.643 -0.127 1.80e-02 3.09e+03 5.01e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       66.00 -    81.69: 1
       81.69 -    97.37: 11
       97.37 -   113.05: 2678
      113.05 -   128.73: 1372
      128.73 -   144.41: 17
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" CB  ARG A 127 "
        model="   7" pdb=" CA  ARG A 127 "
        model="   7" pdb=" HA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     109.00   66.00   43.00 3.00e+00 1.11e-01 2.05e+02
  angle model="   7" pdb=" C   LYS A 125 "
        model="   7" pdb=" N   VAL A 126 "
        model="   7" pdb=" CA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     121.70  144.41  -22.71 1.80e+00 3.09e-01 1.59e+02
  angle model="   7" pdb=" CA  VAL A 126 "
        model="   7" pdb=" C   VAL A 126 "
        model="   7" pdb=" N   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     116.20   93.78   22.42 2.00e+00 2.50e-01 1.26e+02
  angle model="   7" pdb=" C   GLY A 121 "
        model="   7" pdb=" N   ILE A 122 "
        model="   7" pdb=" CA  ILE A 122 "
      ideal   model   delta    sigma   weight residual
     121.70  141.71  -20.01 1.80e+00 3.09e-01 1.24e+02
  angle model="   7" pdb=" N   ILE A 131 "
        model="   7" pdb=" CA  ILE A 131 "
        model="   7" pdb=" CB  ILE A 131 "
      ideal   model   delta    sigma   weight residual
     111.50   93.87   17.63 1.70e+00 3.46e-01 1.07e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.04: 962
       25.04 -    50.07: 36
       50.07 -    75.11: 16
       75.11 -   100.15: 2
      100.15 -   125.18: 5
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   7" pdb=" CA  GLU A 123 "
           model="   7" pdb=" C   GLU A 123 "
           model="   7" pdb=" N   ALA A 124 "
           model="   7" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   54.82  125.18     0      5.00e+00 4.00e-02 6.27e+02
  dihedral model="   7" pdb=" CA  ALA A 124 "
           model="   7" pdb=" C   ALA A 124 "
           model="   7" pdb=" N   LYS A 125 "
           model="   7" pdb=" CA  LYS A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   64.71  115.29     0      5.00e+00 4.00e-02 5.32e+02
  dihedral model="   7" pdb=" CA  LYS A 125 "
           model="   7" pdb=" C   LYS A 125 "
           model="   7" pdb=" N   VAL A 126 "
           model="   7" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   71.07  108.93     0      5.00e+00 4.00e-02 4.75e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.032: 166
       1.032 -    2.064: 2
       2.064 -    3.096: 0
       3.096 -    4.127: 1
       4.127 -    5.159: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CA  HIS A 139 "
            model="   7" pdb=" N   HIS A 139 "
            model="   7" pdb=" C   HIS A 139 "
            model="   7" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.65    5.16 2.00e-01 2.50e+01 6.65e+02
  chirality model="   7" pdb=" CB  THR A  92 "
            model="   7" pdb=" CA  THR A  92 "
            model="   7" pdb=" OG1 THR A  92 "
            model="   7" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.52    5.07 2.00e-01 2.50e+01 6.43e+02
  chirality model="   7" pdb=" CA  TYR A  89 "
            model="   7" pdb=" N   TYR A  89 "
            model="   7" pdb=" C   TYR A  89 "
            model="   7" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.55    5.06 2.00e-01 2.50e+01 6.41e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CA  VAL A 126 "    0.062 2.00e-02 2.50e+03   1.31e-01 1.71e+02
        model="   7" pdb=" C   VAL A 126 "   -0.226 2.00e-02 2.50e+03
        model="   7" pdb=" O   VAL A 126 "    0.097 2.00e-02 2.50e+03
        model="   7" pdb=" N   ARG A 127 "    0.067 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  12 "    0.104 2.00e-02 2.50e+03   4.65e-02 6.50e+01
        model="   7" pdb=" CG  TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  12 "   -0.026 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  12 "    0.095 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  12 "   -0.047 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  12 "   -0.041 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  50 "    0.119 2.00e-02 2.50e+03   4.58e-02 6.29e+01
        model="   7" pdb=" CG  TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  50 "    0.067 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  50 "   -0.042 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  50 "   -0.044 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 45
        2.03 -     2.67: 3060
        2.67 -     3.31: 6653
        3.31 -     3.96: 7834
        3.96 -     4.60: 11927
  Nonbonded interactions: 29519
  Sorted by model distance:
  nonbonded model="   7" pdb=" HA  LYS A 125 "
            model="   7" pdb=" H   ARG A 127 "
     model   vdw
     1.387 2.270
  nonbonded model="   7" pdb=" HA  ALA A 124 "
            model="   7" pdb=" H   VAL A 126 "
     model   vdw
     1.490 2.270
  nonbonded model="   7" pdb="HG23 ILE A  78 "
            model="   7" pdb=" H   LYS A  79 "
     model   vdw
     1.688 2.270
  nonbonded model="   7" pdb="HG23 ILE A 122 "
            model="   7" pdb=" HB2 GLU A 123 "
     model   vdw
     1.719 2.440
  nonbonded model="   7" pdb=" HA  GLU A 123 "
            model="   7" pdb=" HB3 ALA A 124 "
     model   vdw
     1.722 2.440
  ... (remaining 29514 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (51.291, 47.575, 87.362, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (68.811, 46.479, 57.69, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A LEU    2": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  10" pdb=" CB  GLU A 133 "
  Number of C-beta restraints generated:  262

  Time building geometry restraints manager: 1.11 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.892, 56.683, 58.105, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 0.84, per 1000 atoms: 0.38
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (82.123, 41.922, 54.936, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 81
        1.23 -     1.42: 391
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  10" pdb=" CD2 HIS A 139 "
       model="  10" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.66e+00
  bond model="  10" pdb=" CD2 HIS A  43 "
       model="  10" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.27e+00
  bond model="  10" pdb=" CE1 HIS A 139 "
       model="  10" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.99e+00
  bond model="  10" pdb=" CE1 HIS A  43 "
       model="  10" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.75e+00
  bond model="  10" pdb=" CZ  ARG A  58 "
       model="  10" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.74e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       93.75 -   101.59: 4
      101.59 -   109.43: 1308
      109.43 -   117.27: 1750
      117.27 -   125.11: 958
      125.11 -   132.95: 59
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  10" pdb=" C   LEU A 132 "
        model="  10" pdb=" N   GLU A 133 "
        model="  10" pdb=" CA  GLU A 133 "
      ideal   model   delta    sigma   weight residual
     121.70  132.95  -11.25 1.80e+00 3.09e-01 3.91e+01
  angle model="  10" pdb=" N   GLU A 133 "
        model="  10" pdb=" CA  GLU A 133 "
        model="  10" pdb=" HA  GLU A 133 "
      ideal   model   delta    sigma   weight residual
     110.00   93.75   16.25 3.00e+00 1.11e-01 2.93e+01
  angle model="  10" pdb=" OD1 ASN A  72 "
        model="  10" pdb=" CG  ASN A  72 "
        model="  10" pdb=" ND2 ASN A  72 "
      ideal   model   delta    sigma   weight residual
     122.60  117.67    4.93 1.00e+00 1.00e+00 2.43e+01
  angle model="  10" pdb=" C   HIS A 136 "
        model="  10" pdb=" N   HIS A 137 "
        model="  10" pdb=" CA  HIS A 137 "
      ideal   model   delta    sigma   weight residual
     121.70  130.02   -8.32 1.80e+00 3.09e-01 2.14e+01
  angle model="  10" pdb=" OE1 GLN A  66 "
        model="  10" pdb=" CD  GLN A  66 "
        model="  10" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.00    4.60 1.00e+00 1.00e+00 2.12e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.76: 950
       16.76 -    33.51: 51
       33.51 -    50.27: 24
       50.27 -    67.02: 5
       67.02 -    83.78: 1
  Dihedral angle restraints: 1031
    sinusoidal: 562
      harmonic: 469
  Sorted by residual:
  dihedral model="  10" pdb=" CA  ASP A  95 "
           model="  10" pdb=" C   ASP A  95 "
           model="  10" pdb=" N   GLY A  96 "
           model="  10" pdb=" CA  GLY A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  117.52   62.48     0      5.00e+00 4.00e-02 1.56e+02
  dihedral model="  10" pdb=" CA  GLU A 133 "
           model="  10" pdb=" C   GLU A 133 "
           model="  10" pdb=" N   HIS A 134 "
           model="  10" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -140.06  -39.94     0      5.00e+00 4.00e-02 6.38e+01
  dihedral model="  10" pdb=" CA  GLY A  96 "
           model="  10" pdb=" C   GLY A  96 "
           model="  10" pdb=" N   SER A  97 "
           model="  10" pdb=" CA  SER A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.43  -37.57     0      5.00e+00 4.00e-02 5.65e+01
  ... (remaining 1028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.806: 175
       0.806 -    1.611: 0
       1.611 -    2.417: 0
       2.417 -    3.223: 0
       3.223 -    4.029: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CA  GLU A 133 "
            model="  10" pdb=" N   GLU A 133 "
            model="  10" pdb=" C   GLU A 133 "
            model="  10" pdb=" CB  GLU A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.52    4.03 2.00e-01 2.50e+01 4.06e+02
  chirality model="  10" pdb=" CA  ILE A  86 "
            model="  10" pdb=" N   ILE A  86 "
            model="  10" pdb=" C   ILE A  86 "
            model="  10" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality model="  10" pdb=" CA  THR A  82 "
            model="  10" pdb=" N   THR A  82 "
            model="  10" pdb=" C   THR A  82 "
            model="  10" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.30    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A 111 "    0.240 2.00e-02 2.50e+03   9.25e-02 2.57e+02
        model="  10" pdb=" CG  TYR A 111 "   -0.043 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A 111 "   -0.064 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A 111 "   -0.049 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A 111 "    0.128 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A 111 "   -0.115 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A 111 "   -0.070 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A 111 "   -0.033 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  50 "    0.117 2.00e-02 2.50e+03   4.51e-02 6.10e+01
        model="  10" pdb=" CG  TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  50 "   -0.033 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  50 "    0.051 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  50 "   -0.033 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  50 "   -0.062 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  50 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  PHE A  67 "    0.063 2.00e-02 2.50e+03   4.13e-02 5.11e+01
        model="  10" pdb=" CG  PHE A  67 "   -0.017 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 PHE A  67 "    0.002 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 PHE A  67 "   -0.034 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 PHE A  67 "   -0.021 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 PHE A  67 "    0.016 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  PHE A  67 "    0.012 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 PHE A  67 "    0.031 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 PHE A  67 "   -0.079 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 PHE A  67 "   -0.057 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 PHE A  67 "    0.052 2.00e-02 2.50e+03
        model="  10" pdb=" HZ  PHE A  67 "    0.031 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.26: 225
        2.26 -     2.84: 4781
        2.84 -     3.43: 5386
        3.43 -     4.01: 6780
        4.01 -     4.60: 10318
  Nonbonded interactions: 27490
  Sorted by model distance:
  nonbonded model="  10" pdb="HG23 VAL A  41 "
            model="  10" pdb=" H   HIS A  43 "
     model   vdw
     1.671 2.270
  nonbonded model="  10" pdb=" HZ3 LYS A 113 "
            model="  10" pdb=" OD1 ASP A 116 "
     model   vdw
     1.748 1.850
  nonbonded model="  10" pdb="HD13 LEU A  25 "
            model="  10" pdb="HD21 ASN A  72 "
     model   vdw
     1.749 2.270
  nonbonded model="  10" pdb=" OD2 ASP A  36 "
            model="  10" pdb=" HH  TYR A  68 "
     model   vdw
     1.830 1.850
  nonbonded model="  10" pdb=" OE2 GLU A  16 "
            model="  10" pdb=" HZ2 LYS A  19 "
     model   vdw
     1.837 1.850
  ... (remaining 27485 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.616, 61.704, 74.905, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.025, 53.448, 67.026, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  11" pdb=" CB  THR A  83 "
        model="  11" pdb=" CB  HIS A 134 "
        model="  11" pdb=" CB  HIS A 136 "
  Number of C-beta restraints generated:  258

  Time building geometry restraints manager: 0.92 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.543, 42.624, 49.73, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.806, 55.669, 52.525, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 80
        1.23 -     1.42: 393
        1.42 -     1.62: 659
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" N   HIS A 134 "
       model="  11" pdb=" CA  HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.458  1.393  0.065 1.90e-02 2.77e+03 1.16e+01
  bond model="  11" pdb=" CD2 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.410 -0.036 1.10e-02 8.26e+03 1.06e+01
  bond model="  11" pdb=" CE1 HIS A 138 "
       model="  11" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.06e+00
  bond model="  11" pdb=" CD2 HIS A 138 "
       model="  11" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.56e+00
  bond model="  11" pdb=" N   HIS A 135 "
       model="  11" pdb=" CA  HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.458  1.408  0.050 1.90e-02 2.77e+03 7.04e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       92.38 -   100.41: 5
      100.41 -   108.43: 667
      108.43 -   116.46: 2346
      116.46 -   124.49: 967
      124.49 -   132.52: 94
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" C   GLU A 133 "
        model="  11" pdb=" N   HIS A 134 "
        model="  11" pdb=" CA  HIS A 134 "
      ideal   model   delta    sigma   weight residual
     121.70  132.52  -10.82 1.80e+00 3.09e-01 3.61e+01
  angle model="  11" pdb=" OE1 GLN A  66 "
        model="  11" pdb=" CD  GLN A  66 "
        model="  11" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  116.63    5.97 1.00e+00 1.00e+00 3.56e+01
  angle model="  11" pdb=" CA  HIS A 135 "
        model="  11" pdb=" CB  HIS A 135 "
        model="  11" pdb=" CG  HIS A 135 "
      ideal   model   delta    sigma   weight residual
     113.80  108.05    5.75 1.00e+00 1.00e+00 3.31e+01
  angle model="  11" pdb=" C   TYR A  81 "
        model="  11" pdb=" CA  TYR A  81 "
        model="  11" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     109.00   92.38   16.62 3.00e+00 1.11e-01 3.07e+01
  angle model="  11" pdb=" CA  HIS A 134 "
        model="  11" pdb=" CB  HIS A 134 "
        model="  11" pdb=" CG  HIS A 134 "
      ideal   model   delta    sigma   weight residual
     113.80  108.35    5.45 1.00e+00 1.00e+00 2.97e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 936
       17.32 -    34.64: 57
       34.64 -    51.96: 21
       51.96 -    69.28: 10
       69.28 -    86.60: 3
  Dihedral angle restraints: 1027
    sinusoidal: 562
      harmonic: 465
  Sorted by residual:
  dihedral model="  11" pdb=" C   TYR A  81 "
           model="  11" pdb=" N   TYR A  81 "
           model="  11" pdb=" CA  TYR A  81 "
           model="  11" pdb=" CB  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -148.84   26.24     0      2.50e+00 1.60e-01 1.10e+02
  dihedral model="  11" pdb=" N   TYR A  81 "
           model="  11" pdb=" C   TYR A  81 "
           model="  11" pdb=" CA  TYR A  81 "
           model="  11" pdb=" CB  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  147.77  -24.97     0      2.50e+00 1.60e-01 9.98e+01
  dihedral model="  11" pdb=" CA  TYR A  81 "
           model="  11" pdb=" C   TYR A  81 "
           model="  11" pdb=" N   THR A  82 "
           model="  11" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.76   47.24     0      5.00e+00 4.00e-02 8.93e+01
  ... (remaining 1024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.926: 172
       0.926 -    1.851: 1
       1.851 -    2.776: 0
       2.776 -    3.701: 0
       3.701 -    4.625: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  HIS A 136 "
            model="  11" pdb=" N   HIS A 136 "
            model="  11" pdb=" C   HIS A 136 "
            model="  11" pdb=" CB  HIS A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.12    4.63 2.00e-01 2.50e+01 5.35e+02
  chirality model="  11" pdb=" CA  THR A  83 "
            model="  11" pdb=" N   THR A  83 "
            model="  11" pdb=" C   THR A  83 "
            model="  11" pdb=" CB  THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -1.97    4.50 2.00e-01 2.50e+01 5.06e+02
  chirality model="  11" pdb=" CA  HIS A 134 "
            model="  11" pdb=" N   HIS A 134 "
            model="  11" pdb=" C   HIS A 134 "
            model="  11" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.77    4.28 2.00e-01 2.50e+01 4.57e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  89 "   -0.157 2.00e-02 2.50e+03   6.42e-02 1.24e+02
        model="  11" pdb=" CG  TYR A  89 "    0.041 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  89 "    0.038 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  89 "    0.032 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  89 "    0.015 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  89 "    0.023 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  89 "   -0.011 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  89 "   -0.120 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  89 "    0.051 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  89 "    0.031 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  89 "    0.017 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  89 "    0.040 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  50 "   -0.138 2.00e-02 2.50e+03   5.61e-02 9.45e+01
        model="  11" pdb=" CG  TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  50 "    0.033 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  50 "   -0.097 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  50 "    0.058 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  50 "    0.042 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  50 "    0.034 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  81 "   -0.100 2.00e-02 2.50e+03   4.12e-02 5.10e+01
        model="  11" pdb=" CG  TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  81 "    0.028 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  81 "    0.018 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  81 "    0.013 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  81 "   -0.011 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  81 "   -0.058 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  81 "    0.063 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  81 "    0.030 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  81 "   -0.011 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  81 "    0.026 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 117
        2.14 -     2.76: 3860
        2.76 -     3.37: 5891
        3.37 -     3.99: 7200
        3.99 -     4.60: 10743
  Nonbonded interactions: 27811
  Sorted by model distance:
  nonbonded model="  11" pdb=" HG3 GLU A 133 "
            model="  11" pdb=" H   HIS A 134 "
     model   vdw
     1.529 2.270
  nonbonded model="  11" pdb=" HD2 PHE A  15 "
            model="  11" pdb="HE21 GLN A  66 "
     model   vdw
     1.757 2.100
  nonbonded model="  11" pdb=" OD2 ASP A  44 "
            model="  11" pdb=" HG  SER A  46 "
     model   vdw
     1.791 1.850
  nonbonded model="  11" pdb=" HZ2 LYS A  85 "
            model="  11" pdb=" OD1 ASP A  88 "
     model   vdw
     1.805 1.850
  nonbonded model="  11" pdb=" OE1 GLU A  75 "
            model="  11" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.809 1.850
  ... (remaining 27806 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 130}
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.399, 46.676, 51.659, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 0.76, per 1000 atoms: 0.34
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (39.942, 52.119, 71.337, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 92
        1.23 -     1.42: 380
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" ND1 HIS A  43 "
       model="  14" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.10e+00
  bond model="  14" pdb=" CD2 HIS A 139 "
       model="  14" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.42e+00
  bond model="  14" pdb=" CZ  ARG A 129 "
       model="  14" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.46e+00
  bond model="  14" pdb=" ND1 HIS A 135 "
       model="  14" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.32e+00
  bond model="  14" pdb=" CE1 HIS A  43 "
       model="  14" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.28e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.50 -   105.45: 78
      105.45 -   111.40: 2382
      111.40 -   117.35: 599
      117.35 -   123.29: 817
      123.29 -   129.24: 203
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" CB  HIS A 134 "
        model="  14" pdb=" CG  HIS A 134 "
        model="  14" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  125.64    5.56 1.30e+00 5.92e-01 1.83e+01
  angle model="  14" pdb=" OE1 GLN A  66 "
        model="  14" pdb=" CD  GLN A  66 "
        model="  14" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.34    4.26 1.00e+00 1.00e+00 1.81e+01
  angle model="  14" pdb=" CA  ASP A  29 "
        model="  14" pdb=" CB  ASP A  29 "
        model="  14" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.83   -4.23 1.00e+00 1.00e+00 1.79e+01
  angle model="  14" pdb=" CB  HIS A 135 "
        model="  14" pdb=" CG  HIS A 135 "
        model="  14" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.15    5.05 1.30e+00 5.92e-01 1.51e+01
  angle model="  14" pdb=" CA  VAL A  41 "
        model="  14" pdb=" CB  VAL A  41 "
        model="  14" pdb=" CG1 VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.40  117.00   -6.60 1.70e+00 3.46e-01 1.51e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 938
       17.50 -    35.01: 62
       35.01 -    52.51: 19
       52.51 -    70.02: 8
       70.02 -    87.52: 6
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  14" pdb=" CA  SER A  97 "
           model="  14" pdb=" C   SER A  97 "
           model="  14" pdb=" N   SER A  98 "
           model="  14" pdb=" CA  SER A  98 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.42  -25.58     0      5.00e+00 4.00e-02 2.62e+01
  dihedral model="  14" pdb=" CA  ILE A  51 "
           model="  14" pdb=" C   ILE A  51 "
           model="  14" pdb=" N   PRO A  52 "
           model="  14" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.90   23.10     0      5.00e+00 4.00e-02 2.14e+01
  dihedral model="  14" pdb=" CA  TYR A 111 "
           model="  14" pdb=" C   TYR A 111 "
           model="  14" pdb=" N   VAL A 112 "
           model="  14" pdb=" CA  VAL A 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.95  -23.05     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 78
       0.051 -    0.103: 49
       0.103 -    0.154: 30
       0.154 -    0.205: 13
       0.205 -    0.256: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CA  VAL A 126 "
            model="  14" pdb=" N   VAL A 126 "
            model="  14" pdb=" C   VAL A 126 "
            model="  14" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.18    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality model="  14" pdb=" CG  LEU A  53 "
            model="  14" pdb=" CB  LEU A  53 "
            model="  14" pdb=" CD1 LEU A  53 "
            model="  14" pdb=" CD2 LEU A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality model="  14" pdb=" CA  LYS A  85 "
            model="  14" pdb=" N   LYS A  85 "
            model="  14" pdb=" C   LYS A  85 "
            model="  14" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  PHE A  15 "    0.207 2.00e-02 2.50e+03   8.93e-02 2.39e+02
        model="  14" pdb=" CG  PHE A  15 "   -0.012 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 PHE A  15 "   -0.050 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 PHE A  15 "   -0.046 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 PHE A  15 "   -0.015 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 PHE A  15 "   -0.019 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  PHE A  15 "    0.055 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 PHE A  15 "   -0.098 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 PHE A  15 "   -0.085 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 PHE A  15 "   -0.039 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 PHE A  15 "   -0.051 2.00e-02 2.50e+03
        model="  14" pdb=" HZ  PHE A  15 "    0.153 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  50 "    0.178 2.00e-02 2.50e+03   8.36e-02 2.10e+02
        model="  14" pdb=" CG  TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  50 "   -0.035 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  50 "   -0.034 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  50 "   -0.031 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  50 "   -0.033 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  50 "    0.181 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  50 "   -0.067 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  50 "   -0.063 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  50 "   -0.054 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  50 "   -0.059 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A 111 "   -0.171 2.00e-02 2.50e+03   6.78e-02 1.38e+02
        model="  14" pdb=" CG  TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A 111 "    0.036 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A 111 "    0.041 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A 111 "   -0.035 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A 111 "   -0.101 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A 111 "    0.060 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A 111 "    0.076 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A 111 "    0.033 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A 111 "    0.016 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.32: 432
        2.32 -     2.89: 52  Time building chain proxies: 1.22, per 1000 atoms: 0.55
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.622, 43.759, 49.195, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
67
        2.89 -     3.46: 5822
        3.46 -     4.03: 7558
        4.03 -     4.60: 11288
  Nonbonded interactions: 30367
  Sorted by model distance:
  nonbonded model="  14" pdb="HG23 VAL A  41 "
            model="  14" pdb=" H   HIS A  43 "
     model   vdw
     1.744 2.270
  nonbonded model="  14" pdb=" HA  MET A   1 "
            model="  14" pdb=" HE2 MET A   1 "
     model   vdw
     1.787 2.440
  nonbonded model="  14" pdb=" HG  LEU A 132 "
            model="  14" pdb=" H   GLU A 133 "
     model   vdw
     1.825 2.270
  nonbonded model="  14" pdb=" O   LEU A  61 "
            model="  14" pdb=" HG  SER A  65 "
     model   vdw
     1.828 1.850
  nonbonded model="  14" pdb="HD13 LEU A   3 "
            model="  14" pdb="HD11 LEU A  53 "
     model   vdw
     1.855 2.440
  ... (remaining 30362 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.97, per 1000 atoms: 0.44
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (43.555, 71.211, 47.628, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.029, 60.198, 56.942, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.73, 82.519, 54.957, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  PRO A  52 "
        model="   7" pdb=" CB  SER A  90 "
        model="   7" pdb=" CB  VAL A 126 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 1.12 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 62
        1.23 -     1.43: 413
        1.43 -     1.62: 656
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" N   GLY A  80 "
       model="   7" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.576 -0.125 1.60e-02 3.91e+03 6.10e+01
  bond model="   7" pdb=" N   GLU A 123 "
       model="   7" pdb=" CA  GLU A 123 "
    ideal  model  delta    sigma   weight residual
    1.458  1.357  0.101 1.90e-02 2.77e+03 2.81e+01
  bond model="   7" pdb=" CA  LYS A  79 "
       model="   7" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.626 -0.101 2.10e-02 2.27e+03 2.32e+01
  bond model="   7" pdb=" CA  ILE A  78 "
       model="   7" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.427  0.098 2.10e-02 2.27e+03 2.20e+01
  bond model="   7" pdb=" N   SER A 130 "
       model="   7" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.531 -0.073 1.90e-02 2.77e+03 1.49e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       84.10 -    95.66: 7
       95.66 -   107.22: 494
      107.22 -   118.77: 2644
      118.77 -   130.33: 926
      130.33 -   141.89: 8
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" C   LYS A  79 "
        model="   7" pdb=" N   GLY A  80 "
        model="   7" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  141.89  -20.19 1.80e+00 3.09e-01 1.26e+02
  angle model="   7" pdb=" C   MET A 128 "
        model="   7" pdb=" CA  MET A 128 "
        model="   7" pdb=" CB  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.10  127.60  -17.50 1.90e+00 2.77e-01 8.48e+01
  angle model="   7" pdb=" C   TYR A  89 "
        model="   7" pdb=" N   SER A  90 "
        model="   7" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  105.19   16.51 1.80e+00 3.09e-01 8.41e+01
  angle model="   7" pdb=" C   MET A 128 "
        model="   7" pdb=" CA  MET A 128 "
        model="   7" pdb=" HA  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.00   84.10   25.90 3.00e+00 1.11e-01 7.45e+01
  angle model="   7" pdb=" CA  GLU A 123 "
        model="   7" pdb=" C   GLU A 123 "
        model="   7" pdb=" N   ALA A 124 "
      ideal   model   delta    sigma   weight residual
     116.20  100.19   16.01 2.00e+00 2.50e-01 6.41e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.85: 960
       25.85 -    51.70: 48
       51.70 -    77.54: 10
       77.54 -   103.39: 4
      103.39 -   129.24: 3
  Dihedral angle restraints: 1025
    sinusoidal: 562
      harmonic: 463
  Sorted by residual:
  dihedral model="   7" pdb=" CA  LYS A 125 "
           model="   7" pdb=" C   LYS A 125 "
           model="   7" pdb=" N   VAL A 126 "
           model="   7" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   50.76  129.24     0      5.00e+00 4.00e-02 6.68e+02
  dihedral model="   7" pdb=" CA  TYR A  89 "
           model="   7" pdb=" C   TYR A  89 "
           model="   7" pdb=" N   SER A  90 "
           model="   7" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   69.86  110.14     0      5.00e+00 4.00e-02 4.85e+02
  dihedral model="   7" pdb=" CA  MET A 128 "
           model="   7" pdb=" C   MET A 128 "
           model="   7" pdb=" N   ARG A 129 "
           model="   7" pdb=" CA  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -73.34 -106.66     0      5.00e+00 4.00e-02 4.55e+02
  ... (remaining 1022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.003 -    1.013: 169
       1.013 -    2.024: 2
       2.024 -    3.035: 0
       3.035 -    4.045: 1
       4.045 -    5.056: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CB  ILE A 122 "
            model="   7" pdb=" CA  ILE A 122 "
            model="   7" pdb=" CG1 ILE A 122 "
            model="   7" pdb=" CG2 ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.41    5.06 2.00e-01 2.50e+01 6.39e+02
  chirality model="   7" pdb=" CA  PRO A  52 "
            model="   7" pdb=" N   PRO A  52 "
            model="   7" pdb=" C   PRO A  52 "
            model="   7" pdb=" CB  PRO A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72   -2.30    5.02 2.00e-01 2.50e+01 6.30e+02
  chirality model="   7" pdb=" CA  VAL A 126 "
            model="   7" pdb=" N   VAL A 126 "
            model="   7" pdb=" C   VAL A 126 "
            model="   7" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44   -2.57    5.01 2.00e-01 2.50e+01 6.28e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  12 "   -0.099 2.00e-02 2.50e+03   4.52e-02 6.12e+01
        model="   7" pdb=" CG  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  12 "   -0.094 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  12 "    0.045 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  12 "    0.040 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  PHE A  45 "    0.084 2.00e-02 2.50e+03   3.89e-02 4.53e+01
        model="   7" pdb=" CG  PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 PHE A  45 "   -0.028 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 PHE A  45 "   -0.011 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 PHE A  45 "    0.002 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 PHE A  45 "   -0.014 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  PHE A  45 "    0.022 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 PHE A  45 "   -0.065 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 PHE A  45 "   -0.015 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 PHE A  45 "    0.008 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 PHE A  45 "   -0.040 2.00e-02 2.50e+03
        model="   7" pdb=" HZ  PHE A  45 "    0.059 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CA  VAL A 126 "   -0.024 2.00e-02 2.50e+03   5.08e-02 2.58e+01
        model="   7" pdb=" C   VAL A 126 "    0.088 2.00e-02 2.50e+03
        model="   7" pdb=" O   VAL A 126 "   -0.036 2.00e-02 2.50e+03
        model="   7" pdb=" N   ARG A 127 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 208
        2.21 -     2.81: 4517
        2.81 -     3.40: 6457
        3.40 -     4.00: 8034
        4.00 -     4.60: 12280
  Nonbonded interactions: 31496
  Sorted by model distance:
  nonbonded model="   7" pdb="HG23 ILE A  77 "
            model="   7" pdb=" H   LYS A  79 "
     model   vdw
     1.610 2.270
  nonbonded model="   7" pdb="HG23 ILE A  71 "
            model="   7" pdb=" HG3 LYS A  79 "
     model   vdw
     1.712 2.440
  nonbonded model="   7" pdb=" HB2 TYR A  89 "
            model="   7" pdb=" HA  SER A  90 "
     model   vdw
     1.724 2.440
  nonbonded model="   7" pdb=" OD1 ASP A  95 "
            model="   7" pdb=" HG  SER A  97 "
     model   vdw
     1.731 1.850
  nonbonded model="   7" pdb=" OD2 ASP A  36 "
            model="   7" pdb=" HH  TYR A  68 "
     model   vdw
     1.781 1.850
  ... (remaining 31491 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.416, 37.162, 41.697, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.69
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.77 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 0.95, per 1000 atoms: 0.43
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (38.973, 57.689, 82.581, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 128}
  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.298, 46.799, 61.768, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   8" pdb=" N   MET A   1 "
       model="   8" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.44e+00
  bond model="   8" pdb=" CZ  ARG A 127 "
       model="   8" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.326  0.004 1.30e-02 5.92e+03 8.43e-02
  bond model="   8" pdb=" CZ  ARG A 129 "
       model="   8" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 7.06e-02
  bond model="   8" pdb=" CZ  ARG A  21 "
       model="   8" pdb=" NH1 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.98e-02
  bond model="   8" pdb=" NE  ARG A  21 "
       model="   8" pdb=" CZ  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 5.66e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.85 -   106.86: 61
      106.86 -   112.87: 2724
      112.87 -   118.88: 426
      118.88 -   124.89: 824
      124.89 -   130.90: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   8" pdb=" CB  PRO A  22 "
        model="   8" pdb=" CA  PRO A  22 "
        model="   8" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.84   -4.84 3.00e+00 1.11e-01 2.60e+00
  angle model="   8" pdb=" CB  PRO A 114 "
        model="   8" pdb=" CA  PRO A 114 "
        model="   8" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   8" pdb=" CB  PRO A 102 "
        model="   8" pdb=" CA  PRO A 102 "
        model="   8" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.58e+00
  angle model="   8" pdb=" CB  PRO A  54 "
        model="   8" pdb=" CA  PRO A  54 "
        model="   8" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   8" pdb=" CB  PRO A   6 "
        model="   8" pdb=" CA  PRO A   6 "
        model="   8" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 888
       17.45 -    34.89: 77
       34.89 -    52.34: 49
       52.34 -    69.79: 14
       69.79 -    87.23: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   8" pdb=" CB  GLU A   8 "
           model="   8" pdb=" CG  GLU A   8 "
           model="   8" pdb=" CD  GLU A   8 "
           model="   8" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.23   87.23     1      3.00e+01 1.11e-03 1.02e+01
  dihedral model="   8" pdb=" CB  LYS A  79 "
           model="   8" pdb=" CG  LYS A  79 "
           model="   8" pdb=" CD  LYS A  79 "
           model="   8" pdb=" CE  LYS A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.13   59.13     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   8" pdb=" CG  LYS A  27 "
           model="   8" pdb=" CD  LYS A  27 "
           model="   8" pdb=" CE  LYS A  27 "
           model="   8" pdb=" NZ  LYS A  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.10  -59.10     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 90
       0.019 -    0.038: 63
       0.038 -    0.057: 4
       0.057 -    0.076: 0
       0.076 -    0.095: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  ILE A  30 "
            model="   8" pdb=" N   ILE A  30 "
            model="   8" pdb=" C   ILE A  30 "
            model="   8" pdb=" CB  ILE A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.25e-01
  chirality model="   8" pdb=" CA  ILE A  38 "
            model="   8" pdb=" N   ILE A  38 "
            model="   8" pdb=" C   ILE A  38 "
            model="   8" pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.20e-01
  chirality model="   8" pdb=" CA  ILE A  37 "
            model="   8" pdb=" N   ILE A  37 "
            model="   8" pdb=" C   ILE A  37 "
            model="   8" pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.20e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  91 "   -0.001 2.00e-02 2.50e+03   1.35e-03 5.49e-02
        model="   8" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  91 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  81 "   -0.001 2.00e-02 2.50e+03   1.25e-03 4.69e-02
        model="   8" pdb=" CG  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  81 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  PHE A  45 "   -0.001 2.00e-02 2.50e+03   1.24e-03 4.62e-02
        model="   8" pdb=" CG  PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 PHE A  45 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HZ  PHE A  45 "    0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 118
        2.11 -     2.73: 4079
        2.73 -     3.36: 5984
        3.36 -     3.98: 7126
        3.98 -     4.60: 11125
  Nonbonded interactions: 28432
  Sorted by model distance:
  nonbonded model="   8" pdb="HG13 VAL A  41 "
            model="   8" pdb="HD12 ILE A 108 "
     model   vdw
     1.489 2.440
  nonbonded model="   8" pdb="HD23 LEU A   9 "
            model="   8" pdb="HD22 LEU A  26 "
     model   vdw
     1.651 2.440
  nonbonded model="   8" pdb="HG23 VAL A  41 "
            model="   8" pdb=" H   HIS A  43 "
     model   vdw
     1.682 2.270
  nonbonded model="   8" pdb=" HA  LYS A  27 "
            model="   8" pdb="HD12 ILE A  30 "
     model   vdw
     1.753 2.440
  nonbonded model="   8" pdb="HD12 ILE A  37 "
            model="   8" pdb="HD23 LEU A  61 "
     model   vdw
     1.795 2.440
  ... (remaining 28427 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.846, 52.032, 51.067, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.82 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 129}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 87
        1.23 -     1.43: 385
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" CZ  ARG A  21 "
       model="  12" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.74e+00
  bond model="  12" pdb=" CD2 HIS A 139 "
       model="  12" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.43e+00
  bond model="  12" pdb=" CD2 HIS A  43 "
       model="  12" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.05e+00
  bond model="  12" pdb=" CZ  ARG A  58 "
       model="  12" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.00e+00
  bond model="  12" pdb=" CD2 HIS A 138 "
       model="  12" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.81e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.83 -   106.69: 179
      106.69 -   112.54: 2508
      112.54 -   118.40: 451
      118.40 -   124.26: 836
      124.26 -   130.11: 105
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" OE1 GLN A  66 "
        model="  12" pdb=" CD  GLN A  66 "
        model="  12" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.50    5.10 1.00e+00 1.00e+00 2.60e+01
  angle model="  12" pdb=" OE1 GLN A  28 "
        model="  12" pdb=" CD  GLN A  28 "
        model="  12" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.04    4.56 1.00e+00 1.00e+00 2.08e+01
  angle model="  12" pdb=" CA  TYR A 105 "
        model="  12" pdb=" CB  TYR A 105 "
        model="  12" pdb=" CG  TYR A 105 "
      ideal   model   delta    sigma   weight residual
     113.90  121.07   -7.17 1.80e+00 3.09e-01 1.59e+01
  angle model="  12" pdb=" N   PRO A 102 "
        model="  12" pdb=" CA  PRO A 102 "
        model="  12" pdb=" CB  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     103.00  107.32   -4.32 1.10e+00 8.26e-01 1.54e+01
  angle model="  12" pdb=" OE1 GLN A 100 "
        model="  12" pdb=" CD  GLN A 100 "
        model="  12" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.83    3.77 1.00e+00 1.00e+00 1.42e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 945
       17.95 -    35.90: 60
       35.90 -    53.84: 20
       53.84 -    71.79: 7
       71.79 -    89.74: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  12" pdb=" CA  GLU A 133 "
           model="  12" pdb=" C   GLU A 133 "
           model="  12" pdb=" N   HIS A 134 "
           model="  12" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.49  -26.51     0      5.00e+00 4.00e-02 2.81e+01
  dihedral model="  12" pdb=" C   ILE A 108 "
           model="  12" pdb=" N   ILE A 108 "
           model="  12" pdb=" CA  ILE A 108 "
           model="  12" pdb=" CB  ILE A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.06   12.06     0      2.50e+00 1.60e-01 2.33e+01
  dihedral model="  12" pdb=" CA  ALA A 115 "
           model="  12" pdb=" C   ALA A 115 "
           model="  12" pdb=" N   ASP A 116 "
           model="  12" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.62   22.38     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.066: 101
       0.066 -    0.132: 47
       0.132 -    0.198: 24
       0.198 -    0.264: 2
       0.264 -    0.329: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  ILE A 108 "
            model="  12" pdb=" N   ILE A 108 "
            model="  12" pdb=" C   ILE A 108 "
            model="  12" pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.10    0.33 2.00e-01 2.50e+01 2.71e+00
  chirality model="  12" pdb=" CA  LYS A 101 "
            model="  12" pdb=" N   LYS A 101 "
            model="  12" pdb=" C   LYS A 101 "
            model="  12" pdb=" CB  LYS A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality model="  12" pdb=" CB  ILE A  71 "
            model="  12" pdb=" CA  ILE A  71 "
            model="  12" pdb=" CG1 ILE A  71 "
            model="  12" pdb=" CG2 ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A 105 "    0.342 2.00e-02 2.50e+03   1.42e-01 6.04e+02
        model="  12" pdb=" CG  TYR A 105 "   -0.041 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A 105 "   -0.072 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A 105 "   -0.075 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A 105 "   -0.046 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A 105 "   -0.038 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A 105 "    0.027 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A 105 "    0.268 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A 105 "   -0.109 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A 105 "   -0.122 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A 105 "   -0.078 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A 105 "   -0.056 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  89 "    0.109 2.00e-02 2.50e+03   7.47e-02 1.68e+02
        model="  12" pdb=" CG  TYR A  89 "    0.004 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  89 "   -0.029 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  89 "   -0.003 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  89 "   -0.023 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  89 "   -0.053 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  89 "   -0.013 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  89 "    0.181 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  89 "   -0.055 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  89 "    0.025 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  89 "   -0.027 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  89 "   -0.116 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  PHE A  67 "   -0.147 2.00e-02 2.50e+03   6.80e-02 1.39e+02
        model="  12" pdb=" CG  PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 PHE A  67 "    0.052 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 PHE A  67 "    0.018 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 PHE A  67 "   -0.011 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 PHE A  67 "    0.023 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  PHE A  67 "   -0.031 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 PHE A  67 "    0.130 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 PHE A  67 "    0.027 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 PHE A  67 "   -0.040 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 PHE A  67 "    0.061 2.00e-02 2.50e+03
        model="  12" pdb=" HZ  PHE A  67 "   -0.080 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.08: 48
        2.08 -     2.71: 3521
        2.71 -     3.34: 5938
        3.34 -     3.97: 6827
        3.97 -     4.60: 10329
  Nonbonded interactions: 26663
  Sorted by model distance:
  nonbonded model="  12" pdb="HD11 ILE A  71 "
            model="  12" pdb=" H   GLY A  87 "
     model   vdw
     1.456 2.270
  nonbonded model="  12" pdb=" OD1 ASP A  36 "
            model="  12" pdb=" HZ2 LYS A  40 "
     model   vdw
     1.783 1.850
  nonbonded model="  12" pdb=" OE2 GLU A  16 "
            model="  12" pdb=" HZ2 LYS A  19 "
     model   vdw
     1.803 1.850
  nonbonded model="  12" pdb=" HZ1 LYS A  10 "
            model="  12" pdb=" OD1 ASP A  23 "
     model   vdw
     1.805 1.850
  nonbonded model="  12" pdb=" OD2 ASP A  44 "
            model="  12" pdb=" HG  SER A  46 "
     model   vdw
     1.813 1.850
  ... (remaining 26658 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.49e+00
  bond model="   9" pdb=" CZ  ARG A  21 "
       model="   9" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 6.76e-02
  bond model="   9" pdb=" CD  ARG A  21 "
       model="   9" pdb=" NE  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.458  1.461 -0.003 1.40e-02 5.10e+03 5.87e-02
  bond model="   9" pdb=" CZ  ARG A 129 "
       model="   9" pdb=" NH1 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.10e-02
  bond model="   9" pdb=" CZ  ARG A 127 "
       model="   9" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 4.96e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.87 -   106.87: 65
      106.87 -   112.88: 2720
      112.88 -   118.88: 426
      118.88 -   124.89: 824
      124.89 -   130.89: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A 117 "
        model="   9" pdb=" CA  PRO A 117 "
        model="   9" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   9" pdb=" CB  PRO A   6 "
        model="   9" pdb=" CA  PRO A   6 "
        model="   9" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A  52 "
        model="   9" pdb=" CA  PRO A  52 "
        model="   9" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A  54 "
        model="   9" pdb=" CA  PRO A  54 "
        model="   9" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A  22 "
        model="   9" pdb=" CA  PRO A  22 "
        model="   9" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.76: 863
       15.76 -    31.52: 82
       31.52 -    47.28: 50
       47.28 -    63.04: 34
       63.04 -    78.80: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CA  ASP A  95 "
           model="   9" pdb=" CB  ASP A  95 "
           model="   9" pdb=" CG  ASP A  95 "
           model="   9" pdb=" OD1 ASP A  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.08   59.08     1      2.00e+01 2.50e-03 1.17e+01
  dihedral model="   9" pdb=" CA  ASP A  88 "
           model="   9" pdb=" CB  ASP A  88 "
           model="   9" pdb=" CG  ASP A  88 "
           model="   9" pdb=" OD1 ASP A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.82   58.82     1      2.00e+01 2.50e-03 1.16e+01
  dihedral model="   9" pdb=" CA  MET A 128 "
           model="   9" pdb=" CB  MET A 128 "
           model="   9" pdb=" CG  MET A 128 "
           model="   9" pdb=" SD  MET A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.10  -59.90     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 104
       0.019 -    0.038: 51
       0.038 -    0.057: 2
       0.057 -    0.077: 0
       0.077 -    0.096: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A  71 "
            model="   9" pdb=" N   ILE A  71 "
            model="   9" pdb=" C   ILE A  71 "
            model="   9" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.28e-01
  chirality model="   9" pdb=" CA  ILE A 122 "
            model="   9" pdb=" N   ILE A 122 "
            model="   9" pdb=" C   ILE A 122 "
            model="   9" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.26e-01
  chirality model="   9" pdb=" CA  ILE A  51 "
            model="   9" pdb=" N   ILE A  51 "
            model="   9" pdb=" C   ILE A  51 "
            model="   9" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.25e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A 105 "   -0.000 2.00e-02 2.50e+03   1.22e-03 4.48e-02
        model="   9" pdb=" CG  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A 105 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A 105 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A 105 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  45 "   -0.000 2.00e-02 2.50e+03   1.10e-03 3.60e-02
        model="   9" pdb=" CG  PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  45 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A 111 "   -0.001 2.00e-02 2.50e+03   1.03e-03 3.17e-02
        model="   9" pdb=" CG  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 140
        2.14 -     2.76: 430  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.091, 62.469, 46.944, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
6
        2.76 -     3.37: 6001
        3.37 -     3.99: 7206
        3.99 -     4.60: 11048
  Nonbonded interactions: 28701
  Sorted by model distance:
  nonbonded model="   9" pdb="HD23 LEU A   9 "
            model="   9" pdb="HD22 LEU A  26 "
     model   vdw
     1.528 2.440
  nonbonded model="   9" pdb="HG12 VAL A  41 "
            model="   9" pdb=" HA  VAL A 112 "
     model   vdw
     1.708 2.440
  nonbonded model="   9" pdb="HG23 ILE A  37 "
            model="   9" pdb="HG21 ILE A 108 "
     model   vdw
     1.710 2.440
  nonbonded model="   9" pdb=" HA  LYS A  27 "
            model="   9" pdb="HD12 ILE A  30 "
     model   vdw
     1.738 2.440
  nonbonded model="   9" pdb=" HG2 PRO A 117 "
            model="   9" pdb="HD23 LEU A 119 "
     model   vdw
     1.784 2.440
  ... (remaining 28696 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.40e+00
  bond model="   9" pdb=" NE  ARG A  21 "
       model="   9" pdb=" CZ  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 9.09e-02
  bond model="   9" pdb=" CZ  ARG A 129 "
       model="   9" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 6.54e-02
  bond model="   9" pdb=" CZ  ARG A  21 "
       model="   9" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 6.11e-02
  bond model="   9" pdb=" CZ  ARG A  58 "
       model="   9" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.98e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.90 -   106.90: 68
      106.90 -   112.89: 2717
      112.89 -   118.89: 426
      118.89 -   124.89: 824
      124.89 -   130.89: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A  52 "
        model="   9" pdb=" CA  PRO A  52 "
        model="   9" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.84   -4.84 3.00e+00 1.11e-01 2.60e+00
  angle model="   9" pdb=" CB  PRO A 117 "
        model="   9" pdb=" CA  PRO A 117 "
        model="   9" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.59e+00
  angle model="   9" pdb=" CB  PRO A   6 "
        model="   9" pdb=" CA  PRO A   6 "
        model="   9" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A  54 "
        model="   9" pdb=" CA  PRO A  54 "
        model="   9" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A 114 "
        model="   9" pdb=" CA  PRO A 114 "
        model="   9" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.60: 859
       15.60 -    31.21: 88
       31.21 -    46.81: 51
       46.81 -    62.41: 28
       62.41 -    78.01: 6
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CA  LYS A  85 "
           model="   9" pdb=" CB  LYS A  85 "
           model="   9" pdb=" CG  LYS A  85 "
           model="   9" pdb=" CD  LYS A  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.53  -59.53     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   9" pdb=" CA  MET A   1 "
           model="   9" pdb=" CB  MET A   1 "
           model="   9" pdb=" CG  MET A   1 "
           model="   9" pdb=" SD  MET A   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.54   59.46     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   9" pdb=" N   ASP A 116 "
           model="   9" pdb=" CA  ASP A 116 "
           model="   9" pdb=" CB  ASP A 116 "
           model="   9" pdb=" CG  ASP A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -121.42  -58.58     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.019: 100
       0.019 -    0.038: 52
       0.038 -    0.056: 5
       0.056 -    0.075: 0
       0.075 -    0.094: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A 108 "
            model="   9" pdb=" N   ILE A 108 "
            model="   9" pdb=" C   ILE A 108 "
            model="   9" pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.20e-01
  chirality model="   9" pdb=" CA  ILE A  86 "
            model="   9" pdb=" N   ILE A  86 "
            model="   9" pdb=" C   ILE A  86 "
            model="   9" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.17e-01
  chirality model="   9" pdb=" CA  ILE A  78 "
            model="   9" pdb=" N   ILE A  78 "
            model="   9" pdb=" C   ILE A  78 "
            model="   9" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.17e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  68 "    0.001 2.00e-02 2.50e+03   1.26e-03 4.80e-02
        model="   9" pdb=" CG  TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  68 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  68 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  68 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  89 "    0.000 2.00e-02 2.50e+03   1.01e-03 3.09e-02
        model="   9" pdb=" CG  TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  89 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  50 "    0.000 2.00e-02 2.50e+03   8.94e-04 2.40e-02
        model="   9" pdb=" CG  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  50 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.10: 112
        2.10 -     2.73: 4065
        2.73 -     3.35: 6048
        3.35 -     3.98: 7345
        3.98 -     4.60: 11309
  Nonbonded interactions: 28879
  Sorted by model distance:
  nonbonded model="   9" pdb="HD13 LEU A   3 "
            model="   9" pdb="HG21 ILE A  51 "
     model   vdw
     1.476 2.440
  nonbonded model="   9" pdb="HD23 LEU A   9 "
            model="   9" pdb="HD22 LEU A  26 "
     model   vdw
     1.563 2.440
  nonbonded model="   9" pdb="HG13 VAL A  41 "
            model="   9" pdb="HD12 ILE A 108 "
     model   vdw
     1.594 2.440
  nonbonded model="   9" pdb="HG23 ILE A  37 "
            model="   9" pdb="HD13 ILE A 108 "
     model   vdw
     1.704 2.440
  nonbonded model="   9" pdb="HD11 LEU A  93 "
            model="   9" pdb="HD13 LEU A  99 "
     model   vdw
     1.711 2.440
  ... (remaining 28874 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.29, per 1000 atoms: 0.58
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.577, 52.805, 40.929, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.759, 41.908, 56.355, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.07, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (61.95, 53.016, 70.638, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  14" pdb=" CB  LEU A  99 "
  Number of C-beta restraints generated:  262

  Time building geometry restraints manager: 0.73 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 69
        1.23 -     1.42: 403
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" CZ  ARG A  21 "
       model="  14" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.60e+00
  bond model="  14" pdb=" CD2 HIS A 139 "
       model="  14" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.98e+00
  bond model="  14" pdb=" CD2 HIS A 134 "
       model="  14" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.96e+00
  bond model="  14" pdb=" CD2 HIS A  43 "
       model="  14" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.90e+00
  bond model="  14" pdb=" ND1 HIS A 137 "
       model="  14" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.65e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       96.86 -   103.60: 18
      103.60 -   110.34: 2192
      110.34 -   117.08: 839
      117.08 -   123.82: 899
      123.82 -   130.55: 131
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" C   SER A  98 "
        model="  14" pdb=" N   LEU A  99 "
        model="  14" pdb=" CA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     121.70  130.55   -8.85 1.80e+00 3.09e-01 2.42e+01
  angle model="  14" pdb=" OE1 GLN A 100 "
        model="  14" pdb=" CD  GLN A 100 "
        model="  14" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  117.79    4.81 1.00e+00 1.00e+00 2.31e+01
  angle model="  14" pdb=" OE1 GLN A  66 "
        model="  14" pdb=" CD  GLN A  66 "
        model="  14" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.03    4.57 1.00e+00 1.00e+00 2.09e+01
  angle model="  14" pdb=" OG1 THR A  56 "
        model="  14" pdb=" CB  THR A  56 "
        model="  14" pdb=" CG2 THR A  56 "
      ideal   model   delta    sigma   weight residual
     109.30  100.78    8.52 2.00e+00 2.50e-01 1.81e+01
  angle model="  14" pdb=" CA  THR A  56 "
        model="  14" pdb=" CB  THR A  56 "
        model="  14" pdb=" OG1 THR A  56 "
      ideal   model   delta    sigma   weight residual
     109.60  115.94   -6.34 1.50e+00 4.44e-01 1.79e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 935
       17.13 -    34.27: 59
       34.27 -    51.40: 21
       51.40 -    68.53: 11
       68.53 -    85.67: 5
  Dihedral angle restraints: 1031
    sinusoidal: 562
      harmonic: 469
  Sorted by residual:
  dihedral model="  14" pdb=" CA  GLU A 120 "
           model="  14" pdb=" C   GLU A 120 "
           model="  14" pdb=" N   GLY A 121 "
           model="  14" pdb=" CA  GLY A 121 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.54  -26.46     0      5.00e+00 4.00e-02 2.80e+01
  dihedral model="  14" pdb=" CA  HIS A 138 "
           model="  14" pdb=" C   HIS A 138 "
           model="  14" pdb=" N   HIS A 139 "
           model="  14" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.70   25.30     0      5.00e+00 4.00e-02 2.56e+01
  dihedral model="  14" pdb=" CA  LEU A  93 "
           model="  14" pdb=" C   LEU A  93 "
           model="  14" pdb=" N   GLY A  94 "
           model="  14" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.02  -21.98     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 1028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.930: 175
       0.930 -    1.860: 0
       1.860 -    2.790: 0
       2.790 -    3.720: 0
       3.720 -    4.650: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CA  LEU A  99 "
            model="  14" pdb=" N   LEU A  99 "
            model="  14" pdb=" C   LEU A  99 "
            model="  14" pdb=" CB  LEU A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.14    4.65 2.00e-01 2.50e+01 5.40e+02
  chirality model="  14" pdb=" CB  THR A  56 "
            model="  14" pdb=" CA  THR A  56 "
            model="  14" pdb=" OG1 THR A  56 "
            model="  14" pdb=" CG2 THR A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality model="  14" pdb=" CA  LYS A 101 "
            model="  14" pdb=" N   LYS A 101 "
            model="  14" pdb=" C   LYS A 101 "
            model="  14" pdb=" CB  LYS A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  50 "    0.228 2.00e-02 2.50e+03   9.57e-02 2.75e+02
        model="  14" pdb=" CG  TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  50 "   -0.050 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  50 "   -0.047 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  50 "    0.178 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  50 "   -0.088 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  50 "   -0.080 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  50 "   -0.046 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  50 "   -0.052 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  91 "    0.171 2.00e-02 2.50e+03   6.79e-02 1.38e+02
        model="  14" pdb=" CG  TYR A  91 "   -0.031 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  91 "   -0.051 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  91 "   -0.030 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  91 "   -0.021 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  91 "    0.015 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  91 "    0.092 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  91 "   -0.096 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  91 "   -0.035 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  91 "    0.023 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  91 "   -0.039 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  12 "    0.137 2.00e-02 2.50e+03   6.61e-02 1.31e+02
        model="  14" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  12 "   -0.031 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  12 "   -0.024 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  12 "   -0.032 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  12 "    0.149 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  12 "   -0.057 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  12 "   -0.030 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  12 "   -0.032 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  12 "   -0.056 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 415
        2.32 -     2.89: 5098
        2.89 -     3.46: 5329
        3.46 -     4.03: 6688
        4.03 -     4.60: 9775
  Nonbonded interactions: 27305
  Sorted by model distance:
  nonbonded model="  14" pdb=" OE2 GLU A  16 "
            model="  14" pdb=" HZ2 LYS A  19 "
     model   vdw
     1.749 1.850
  nonbonded model="  14" pdb=" OD1 ASP A  36 "
            model="  14" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.812 1.850
  nonbonded model="  14" pdb=" O   ILE A  30 "
            model="  14" pdb=" HG1 THR A  34 "
     model   vdw
     1.827 1.850
  nonbonded model="  14" pdb=" O   LEU A  61 "
            model="  14" pdb=" HG  SER A  65 "
     model   vdw
     1.838 1.850
  nonbonded model="  14" pdb=" OD2 ASP A  44 "
            model="  14" pdb=" HG  SER A  46 "
     model   vdw
     1.844 1.850
  ... (remaining 27300 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.912, 50.215, 47.769, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   0" pdb=" CB  ILE A  51 "
        model="   0" pdb=" CB  ASP A  74 "
        model="   0" pdb=" CB  ILE A  78 "
        model="   0" pdb=" CB  LYS A  79 "
        model="   0" pdb=" CB  TYR A  89 "
        model="   0" pdb=" CB  THR A  92 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  LYS A  79 "
        model="   7" pdb=" CB  GLU A 123 "
        model="   7" pdb=" CB  LYS A 125 "
        model="   7" pdb=" CB  VAL A 126 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 0.91, per 1000 atoms: 0.41
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.696, 60.141, 56.562, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  14" pdb=" CB  GLU A  84 "
        model="  14" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 1.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 99
        1.23 -     1.43: 374
        1.43 -     1.63: 654
        1.63 -     1.82: 9
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" N   TYR A  91 "
       model="   0" pdb=" CA  TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.458  1.594 -0.136 1.90e-02 2.77e+03 5.14e+01
  bond model="   0" pdb=" CB  THR A  92 "
       model="   0" pdb=" OG1 THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.433  1.329  0.104 1.60e-02 3.91e+03 4.20e+01
  bond model="   0" pdb=" C   SER A  90 "
       model="   0" pdb=" N   TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.329  1.416 -0.087 1.40e-02 5.10e+03 3.83e+01
  bond model="   0" pdb=" N   LYS A  79 "
       model="   0" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.570 -0.112 1.90e-02 2.77e+03 3.47e+01
  bond model="   0" pdb=" CB  LEU A  93 "
       model="   0" pdb=" CG  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.646 -0.116 2.00e-02 2.50e+03 3.39e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       79.51 -    93.23: 12
       93.23 -   106.94: 251
      106.94 -   120.65: 3270
      120.65 -   134.37: 535
      134.37 -   148.08: 11
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  THR A  92 "
        model="   0" pdb=" CB  THR A  92 "
        model="   0" pdb=" CG2 THR A  92 "
      ideal   model   delta    sigma   weight residual
     110.50  146.85  -36.35 1.70e+00 3.46e-01 4.57e+02
  angle model="   0" pdb=" CA  ILE A  78 "
        model="   0" pdb=" CB  ILE A  78 "
        model="   0" pdb=" CG2 ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.50  138.35  -27.85 1.70e+00 3.46e-01 2.68e+02
  angle model="   0" pdb=" C   ILE A  78 "
        model="   0" pdb=" CA  ILE A  78 "
        model="   0" pdb=" CB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     111.60  139.42  -27.82 2.00e+00 2.50e-01 1.94e+02
  angle model="   0" pdb=" OG1 THR A  92 "
        model="   0" pdb=" CB  THR A  92 "
        model="   0" pdb=" HB  THR A  92 "
      ideal   model   delta    sigma   weight residual
     109.00  148.08  -39.08 3.00e+00 1.11e-01 1.70e+02
  angle model="   0" pdb=" N   LEU A  93 "
        model="   0" pdb=" CA  LEU A  93 "
        model="   0" pdb=" CB  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.50  127.73  -17.23 1.70e+00 3.46e-01 1.03e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.13: 969
       26.13 -    52.26: 39
       52.26 -    78.39: 10
       78.39 -   104.52: 2
      104.52 -   130.64: 1
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -49.36 -130.64     0      5.00e+00 4.00e-02 6.83e+02
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   77.19  102.81     0      5.00e+00 4.00e-02 4.23e+02
  dihedral model="   0" pdb=" CA  GLY A  73 "
           model="   0" pdb=" C   GLY A  73 "
           model="   0" pdb=" N   ASP A  74 "
           model="   0" pdb=" CA  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -121.65  -58.35     0      5.00e+00 4.00e-02 1.36e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.020: 167
       1.020 -    2.039: 2
       2.039 -    3.058: 0
       3.058 -    4.077: 2
       4.077 -    5.096: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  89 "
            model="   0" pdb=" N   TYR A  89 "
            model="   0" pdb=" C   TYR A  89 "
            model="   0" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.59    5.10 2.00e-01 2.50e+01 6.49e+02
  chirality model="   0" pdb=" CA  LYS A  79 "
            model="   0" pdb=" N   LYS A  79 "
            model="   0" pdb=" C   LYS A  79 "
            model="   0" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.51    5.02 2.00e-01 2.50e+01 6.29e+02
  chirality model="   0" pdb=" CA  THR A  92 "
            model="   0" pdb=" N   THR A  92 "
            model="   0" pdb=" C   THR A  92 "
            model="   0" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.17    4.69 2.00e-01 2.50e+01 5.51e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.139 2.00e-02 2.50e+03   5.87e-02 1.03e+02
        model="   0" pdb=" CG  TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.114 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.031 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.143 2.00e-02 2.50e+03   5.32e-02 8.48e+01
        model="   0" pdb=" CG  TYR A  50 "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.110 2.00e-02 2.50e+03   4.40e-02 5.81e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.078 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.37 -     2.02: 51
        2.02 -     2.66: 3041
        2.66 -     3.31: 6826
        3.31 -     3.95: 8120
        3.95 -     4.60: 12229
  Nonbonded interactions: 30267
  Sorted by model distance:
  nonbonded model="   0" pdb=" H   THR A  92 "
            model="   0" pdb=" HA  SER A  98 "
     model   vdw
     1.372 2.270
  nonbonded model="   0" pdb="HG22 ILE A  78 "
            model="   0" pdb=" HA  TYR A  81 "
     model   vdw
     1.639 2.440
  nonbonded model="   0" pdb=" HA2 GLY A  80 "
            model="   0" pdb="HG21 THR A  92 "
     model   vdw
     1.653 2.440
  nonbonded model="   0" pdb=" HB  THR A  92 "
            model="   0" pdb="HG22 THR A  92 "
     model   vdw
     1.674 1.952
  nonbonded model="   0" pdb="HG22 THR A  92 "
            model="   0" pdb="HD12 LEU A  93 "
     model   vdw
     1.676 2.440
  ... (remaining 30262 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  14" pdb=" CB  GLU A  75 "
        model="  14" pdb=" CB  LEU A  99 "
        model="  14" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  258

  Time building geometry restraints manager: 1.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 44
        1.23 -     1.42: 429
        1.42 -     1.62: 659
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" CA  LYS A 125 "
       model="   7" pdb=" C   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.525  1.432  0.093 2.10e-02 2.27e+03 1.96e+01
  bond model="   7" pdb=" N   GLU A 123 "
       model="   7" pdb=" CA  GLU A 123 "
    ideal  model  delta    sigma   weight residual
    1.458  1.542 -0.084 1.90e-02 2.77e+03 1.94e+01
  bond model="   7" pdb=" C   LYS A 125 "
       model="   7" pdb=" N   VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.329  1.271  0.058 1.40e-02 5.10e+03 1.69e+01
  bond model="   7" pdb=" N   VAL A 126 "
       model="   7" pdb=" CA  VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.384  0.074 1.90e-02 2.77e+03 1.53e+01
  bond model="   7" pdb=" CA  ARG A 127 "
       model="   7" pdb=" C   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.525  1.466  0.059 2.10e-02 2.27e+03 7.76e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       86.56 -    97.43: 12
       97.43 -   108.29: 663
      108.29 -   119.15: 2514
      119.15 -   130.01: 884
      130.01 -   140.87: 6
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" C   ILE A  77 "
        model="   7" pdb=" N   ILE A  78 "
        model="   7" pdb=" CA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     121.70  140.87  -19.17 1.80e+00 3.09e-01 1.13e+02
  angle model="   7" pdb=" CB  HIS A 135 "
        model="   7" pdb=" CG  HIS A 135 "
        model="   7" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  118.31   12.89 1.30e+00 5.92e-01 9.83e+01
  angle model="   7" pdb=" C   ASP A  74 "
        model="   7" pdb=" CA  ASP A  74 "
        model="   7" pdb=" CB  ASP A  74 "
      ideal   model   delta    sigma   weight residual
     110.10  128.30  -18.20 1.90e+00 2.77e-01 9.18e+01
  angle model="   7" pdb=" C   ILE A  78 "
        model="   7" pdb=" N   LYS A  79 "
        model="   7" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  136.43  -14.73 1.80e+00 3.09e-01 6.69e+01
  angle model="   7" pdb=" C   ALA A 124 "
        model="   7" pdb=" CA  ALA A 124 "
        model="   7" pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     110.50  122.57  -12.07 1.50e+00 4.44e-01 6.47e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 910
       17.19 -    34.37: 74
       34.37 -    51.56: 27
       51.56 -    68.74: 9
       68.74 -    85.93: 3
  Dihedral angle restraints: 1023
    sinusoidal: 562
      harmonic: 461
  Sorted by residual:
  dihedral model="   7" pdb=" CA  GLU A 123 "
           model="   7" pdb=" C   GLU A 123 "
           model="   7" pdb=" N   ALA A 124 "
           model="   7" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -94.07  -85.93     0      5.00e+00 4.00e-02 2.95e+02
  dihedral model="   7" pdb=" CA  LEU A 119 "
           model="   7" pdb=" C   LEU A 119 "
           model="   7" pdb=" N   GLU A 120 "
           model="   7" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  103.09   76.91     0      5.00e+00 4.00e-02 2.37e+02
  dihedral model="   7" pdb=" C   ALA A 124 "
           model="   7" pdb=" N   ALA A 124 "
           model="   7" pdb=" CA  ALA A 124 "
           model="   7" pdb=" CB  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -158.16   35.56     0      2.50e+00 1.60e-01 2.02e+02
  ... (remaining 1020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.073: 168
       1.073 -    2.145: 1
       2.145 -    3.217: 0
       3.217 -    4.290: 2
       4.290 -    5.362: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CA  GLU A 123 "
            model="   7" pdb=" N   GLU A 123 "
            model="   7" pdb=" C   GLU A 123 "
            model="   7" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.85    5.36 2.00e-01 2.50e+01 7.19e+02
  chirality model="   7" pdb=" CB  ILE A  78 "
            model="   7" pdb=" CA  ILE A  78 "
            model="   7" pdb=" CG1 ILE A  78 "
            model="   7" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.66    5.30 2.00e-01 2.50e+01 7.03e+02
  chirality model="   7" pdb=" CB  ILE A 131 "
            model="   7" pdb=" CA  ILE A 131 "
            model="   7" pdb=" CG1 ILE A 131 "
            model="   7" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.34    4.98 2.00e-01 2.50e+01 6.20e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  91 "   -0.286 2.00e-02 2.50e+03   1.37e-01 5.63e+02
        model="   7" pdb=" CG  TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  91 "    0.058 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  91 "    0.051 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  91 "    0.051 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  91 "    0.052 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  91 "   -0.049 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  91 "   -0.293 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  91 "    0.101 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  91 "    0.085 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  91 "    0.111 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  91 "    0.119 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  HIS A 135 "   -0.137 2.00e-02 2.50e+03   7.92e-02 1.25e+02
        model="   7" pdb=" CG  HIS A 135 "    0.099 2.00e-02 2.50e+03
        model="   7" pdb=" ND1 HIS A 135 "    0.109 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 HIS A 135 "    0.028 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 HIS A 135 "   -0.014 2.00e-02 2.50e+03
        model="   7" pdb=" NE2 HIS A 135 "   -0.057 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 HIS A 135 "    0.035 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 HIS A 135 "   -0.063 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  89 "   -0.148 2.00e-02 2.50e+03   6.33e-02 1.20e+02
        model="   7" pdb=" CG  TYR A  89 "    0.096 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  89 "    0.056 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  89 "    0.028 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  89 "   -0.020 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  89 "    0.007 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  89 "   -0.009 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  89 "    0.080 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  89 "   -0.003 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  89 "   -0.078 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  89 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 251
        2.23 -     2.82: 4693
        2.82 -     3.42: 6300
        3.42 -     4.01: 7853
        4.01 -     4.60: 11630
  Nonbonded interactions: 30727
  Sorted by model distance:
  nonbonded model="   7" pdb=" H   GLU A 123 "
            model="   7" pdb=" H   LYS A 125 "
     model   vdw
     1.639 2.100
  nonbonded model="   7" pdb=" HA  LEU A 132 "
            model="   7" pdb=" HD2 HIS A 135 "
     model   vdw
     1.688 2.270
  nonbonded model="   7" pdb=" HA  GLU A 123 "
            model="   7" pdb=" HB3 LYS A 125 "
     model   vdw
     1.737 2.440
  nonbonded model="   7" pdb=" OD2 ASP A  36 "
            model="   7" pdb=" HH  TYR A  68 "
     model   vdw
     1.739 1.850
  nonbonded model="   7" pdb=" OD1 ASP A  74 "
            model="   7" pdb=" HG  SER A  76 "
     model   vdw
     1.763 1.850
  ... (remaining 30722 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 75
        1.23 -     1.42: 397
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" CD2 HIS A 139 "
       model="  14" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.52e+00
  bond model="  14" pdb=" CD2 HIS A 138 "
       model="  14" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.47e+00
  bond model="  14" pdb=" CZ  ARG A 127 "
       model="  14" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.10e+00
  bond model="  14" pdb=" CD2 HIS A 134 "
       model="  14" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.94e+00
  bond model="  14" pdb=" CZ  ARG A  21 "
       model="  14" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.85e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.20 -   104.56: 46
      104.56 -   110.91: 2277
      110.91 -   117.26: 724
      117.26 -   123.61: 880
      123.61 -   129.97: 152
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" CA  HIS A 139 "
        model="  14" pdb=" CB  HIS A 139 "
        model="  14" pdb=" CG  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     113.80  124.10  -10.30 1.00e+00 1.00e+00 1.06e+02
  angle model="  14" pdb=" CA  HIS A 138 "
        model="  14" pdb=" CB  HIS A 138 "
        model="  14" pdb=" CG  HIS A 138 "
      ideal   model   delta    sigma   weight residual
     113.80  118.71   -4.91 1.00e+00 1.00e+00 2.41e+01
  angle model="  14" pdb=" C   HIS A 139 "
        model="  14" pdb=" CA  HIS A 139 "
        model="  14" pdb=" CB  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     110.10  118.91   -8.81 1.90e+00 2.77e-01 2.15e+01
  angle model="  14" pdb=" C   THR A  83 "
        model="  14" pdb=" N   GLU A  84 "
        model="  14" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  129.97   -8.27 1.80e+00 3.09e-01 2.11e+01
  angle model="  14" pdb=" OE1 GLN A  28 "
        model="  14" pdb=" CD  GLN A  28 "
        model="  14" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.13    4.47 1.00e+00 1.00e+00 1.99e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 951
       17.68 -    35.36: 53
       35.36 -    53.04: 12
       53.04 -    70.72: 8
       70.72 -    88.40: 5
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  14" pdb=" C   THR A  83 "
           model="  14" pdb=" N   THR A  83 "
           model="  14" pdb=" CA  THR A  83 "
           model="  14" pdb=" CB  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -141.15   19.15     0      2.50e+00 1.60e-01 5.87e+01
  dihedral model="  14" pdb=" N   THR A  83 "
           model="  14" pdb=" C   THR A  83 "
           model="  14" pdb=" CA  THR A  83 "
           model="  14" pdb=" CB  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  141.08  -17.68     0      2.50e+00 1.60e-01 5.00e+01
  dihedral model="  14" pdb=" C   GLU A 120 "
           model="  14" pdb=" N   GLU A 120 "
           model="  14" pdb=" CA  GLU A 120 "
           model="  14" pdb=" CB  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.46   14.86     0      2.50e+00 1.60e-01 3.53e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.942: 174
       0.942 -    1.884: 0
       1.884 -    2.826: 0
       2.826 -    3.768: 0
       3.768 -    4.710: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CA  GLU A  84 "
            model="  14" pdb=" N   GLU A  84 "
            model="  14" pdb=" C   GLU A  84 "
            model="  14" pdb=" CB  GLU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.20    4.71 2.00e-01 2.50e+01 5.55e+02
  chirality model="  14" pdb=" CA  HIS A 139 "
            model="  14" pdb=" N   HIS A 139 "
            model="  14" pdb=" C   HIS A 139 "
            model="  14" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.71    4.22 2.00e-01 2.50e+01 4.46e+02
  chirality model="  14" pdb=" CA  THR A  83 "
            model="  14" pdb=" N   THR A  83 "
            model="  14" pdb=" C   THR A  83 "
            model="  14" pdb=" CB  THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.72    0.80 2.00e-01 2.50e+01 1.61e+01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  50 "    0.208 2.00e-02 2.50e+03   8.79e-02 2.32e+02
        model="  14" pdb=" CG  TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  50 "   -0.038 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  50 "   -0.049 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  50 "   -0.033 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  50 "    0.171 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  50 "   -0.057 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  50 "   -0.087 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  50 "   -0.057 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  50 "   -0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  HIS A 139 "   -0.103 2.00e-02 2.50e+03   6.19e-02 7.65e+01
        model="  14" pdb=" CG  HIS A 139 "    0.113 2.00e-02 2.50e+03
        model="  14" pdb=" ND1 HIS A 139 "    0.061 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 HIS A 139 "    0.020 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 HIS A 139 "   -0.012 2.00e-02 2.50e+03
        model="  14" pdb=" NE2 HIS A 139 "   -0.035 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 HIS A 139 "   -0.002 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 HIS A 139 "   -0.042 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  ASN A  72 "    0.063 2.00e-02 2.50e+03   5.46e-02 4.46e+01
        model="  14" pdb=" CG  ASN A  72 "   -0.072 2.00e-02 2.50e+03
        model="  14" pdb=" OD1 ASN A  72 "   -0.010 2.00e-02 2.50e+03
        model="  14" pdb=" ND2 ASN A  72 "   -0.007 2.00e-02 2.50e+03
        model="  14" pdb="HD21 ASN A  72 "    0.078 2.00e-02 2.50e+03
        model="  14" pdb="HD22 ASN A  72 "   -0.050 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.35: 567
        2.35 -     2.91: 4989
        2.91 -     3.47: 5389
        3.47 -     4.04: 6992
        4.04 -     4.60: 10280
  Nonbonded interactions: 28217
  Sorted by model distance:
  nonbonded model="  14" pdb="HD22 LEU A  70 "
            model="  14" pdb=" HG3 GLU A  84 "
     model   vdw
     1.783 2.440
  nonbonded model="  14" pdb=" HG  SER A  46 "
            model="  14" pdb=" OE2 GLU A 120 "
     model   vdw
     1.810 1.850
  nonbonded model="  14" pdb=" O   ILE A  30 "
            model="  14" pdb=" HG1 THR A  34 "
     model   vdw
     1.839 1.850
  nonbonded model="  14" pdb=" HZ2 LYS A  63 "
            model="  14" pdb=" OD1 ASP A 103 "
     model   vdw
     1.848 1.850
  nonbonded model="  14" pdb=" O   ASP A  36 "
            model="  14" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.849 1.850
  ... (remaining 28212 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 84
        1.23 -     1.42: 388
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" CZ  ARG A  21 "
       model="  14" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.98e+00
  bond model="  14" pdb=" CD2 HIS A  43 "
       model="  14" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.73e+00
  bond model="  14" pdb=" CD2 HIS A 134 "
       model="  14" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.47e+00
  bond model="  14" pdb=" ND1 HIS A 139 "
       model="  14" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.82e+00
  bond model="  14" pdb=" CE1 HIS A  43 "
       model="  14" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.52e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       91.70 -   100.22: 3
      100.22 -   108.74: 805
      108.74 -   117.26: 2249
      117.26 -   125.79: 974
      125.79 -   134.31: 48
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" C   SER A  98 "
        model="  14" pdb=" N   LEU A  99 "
        model="  14" pdb=" CA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     121.70  134.31  -12.61 1.80e+00 3.09e-01 4.91e+01
  angle model="  14" pdb=" C   LEU A 132 "
        model="  14" pdb=" N   GLU A 133 "
        model="  14" pdb=" CA  GLU A 133 "
      ideal   model   delta    sigma   weight residual
     121.70  132.59  -10.89 1.80e+00 3.09e-01 3.66e+01
  angle model="  14" pdb=" C   LEU A  99 "
        model="  14" pdb=" CA  LEU A  99 "
        model="  14" pdb=" HA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     109.00   91.70   17.30 3.00e+00 1.11e-01 3.33e+01
  angle model="  14" pdb=" OE1 GLN A  66 "
        model="  14" pdb=" CD  GLN A  66 "
        model="  14" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.98    4.62 1.00e+00 1.00e+00 2.13e+01
  angle model="  14" pdb=" C   LEU A  99 "
        model="  14" pdb=" CA  LEU A  99 "
        model="  14" pdb=" CB  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     110.10  118.49   -8.39 1.90e+00 2.77e-01 1.95e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.19: 947
       18.19 -    36.39: 44
       36.39 -    54.58: 21
       54.58 -    72.77: 6
       72.77 -    90.97: 9
  Dihedral angle restraints: 1027
    sinusoidal: 562
      harmonic: 465
  Sorted by residual:
  dihedral model="  14" pdb=" CA  LEU A  99 "
           model="  14" pdb=" C   LEU A  99 "
           model="  14" pdb=" N   GLN A 100 "
           model="  14" pdb=" CA  GLN A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.68  -35.32     0      5.00e+00 4.00e-02 4.99e+01
  dihedral model="  14" pdb=" CA  SER A  97 "
           model="  14" pdb=" C   SER A  97 "
           model="  14" pdb=" N   SER A  98 "
           model="  14" pdb=" CA  SER A  98 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.24  -30.76     0      5.00e+00 4.00e-02 3.78e+01
  dihedral model="  14" pdb=" C   HIS A 134 "
           model="  14" pdb=" N   HIS A 134 "
           model="  14" pdb=" CA  HIS A 134 "
           model="  14" pdb=" CB  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.23   11.63     0      2.50e+00 1.60e-01 2.16e+01
  ... (remaining 1024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.931: 173
       0.931 -    1.862: 0
       1.862 -    2.793: 0
       2.793 -    3.724: 0
       3.724 -    4.655: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CA  HIS A 139 "
            model="  14" pdb=" N   HIS A 139 "
            model="  14" pdb=" C   HIS A 139 "
            model="  14" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.15    4.66 2.00e-01 2.50e+01 5.42e+02
  chirality model="  14" pdb=" CA  GLU A  75 "
            model="  14" pdb=" N   GLU A  75 "
            model="  14" pdb=" C   GLU A  75 "
            model="  14" pdb=" CB  GLU A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.86    4.37 2.00e-01 2.50e+01 4.77e+02
  chirality model="  14" pdb=" CA  LEU A  99 "
            model="  14" pdb=" N   LEU A  99 "
            model="  14" pdb=" C   LEU A  99 "
            model="  14" pdb=" CB  LEU A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.36    3.87 2.00e-01 2.50e+01 3.74e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  50 "    0.166 2.00e-02 2.50e+03   7.49e-02 1.68e+02
        model="  14" pdb=" CG  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  50 "   -0.039 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  50 "   -0.032 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  50 "    0.153 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  50 "   -0.045 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  50 "   -0.079 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  50 "   -0.060 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  50 "   -0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  89 "   -0.152 2.00e-02 2.50e+03   6.84e-02 1.41e+02
        model="  14" pdb=" CG  TYR A  89 "   -0.023 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  89 "    0.021 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  89 "    0.045 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  89 "    0.022 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  89 "   -0.003 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  89 "   -0.031 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  89 "   -0.090 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  89 "    0.048 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  89 "    0.122 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  89 "    0.057 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  89 "   -0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A 111 "   -0.134 2.00e-02 2.50e+03   5.31e-02 8.44e+01
        model="  14" pdb=" CG  TYR A 111 "    0.025 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A 111 "    0.024 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A 111 "    0.041 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A 111 "   -0.062 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A 111 "    0.029 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A 111 "    0.081 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A 111 "   -0.031 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.33: 387
        2.33 -     2.89: 5047
        2.89 -     3.46: 5217
        3.46 -     4.03: 6879
        4.03 -     4.60: 10184
  Nonbonded interactions: 27714
  Sorted by model distance:
  nonbonded model="  14" pdb=" H   LEU A  93 "
            model="  14" pdb=" HB3 ASP A 103 "
     model   vdw
     1.757 2.270
  nonbonded model="  14" pdb=" OD1 ASP A 110 "
            model="  14" pdb=" HZ3 LYS A 113 "
     model   vdw
     1.828 1.850
  nonbonded model="  14" pdb=" OD1 ASP A  95 "
            model="  14" pdb=" HG  SER A  98 "
     model   vdw
     1.831 1.850
  nonbonded model="  14" pdb=" HZ3 LYS A  10 "
            model="  14" pdb=" OD2 ASP A  23 "
     model   vdw
     1.844 1.850
  nonbonded model="  14" pdb=" O   LEU A  61 "
            model="  14" pdb=" HG  SER A  65 "
     model   vdw
     1.846 1.850
  ... (remaining 27709 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  ILE A  77 "
        model="   7" pdb=" CB  LYS A  79 "
        model="   7" pdb=" CB  THR A  92 "
        model="   7" pdb=" CB  LEU A 119 "
        model="   7" pdb=" CB  ILE A 122 "
        model="   7" pdb=" CB  ALA A 124 "
        model="   7" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  11" pdb=" CB  ILE A 108 "
        model="  11" pdb=" CB  TYR A 111 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 0.95 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.26, per 1000 atoms: 0.57
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (39.5, 46.832, 72.913, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 74
        1.23 -     1.43: 400
        1.43 -     1.62: 656
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" CA  GLY A 121 "
       model="   7" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.674 -0.158 1.80e-02 3.09e+03 7.75e+01
  bond model="   7" pdb=" N   ARG A 127 "
       model="   7" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.625 -0.167 1.90e-02 2.77e+03 7.71e+01
  bond model="   7" pdb=" N   ILE A 122 "
       model="   7" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.616 -0.158 1.90e-02 2.77e+03 6.92e+01
  bond model="   7" pdb=" N   MET A 128 "
       model="   7" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.583 -0.125 1.90e-02 2.77e+03 4.33e+01
  bond model="   7" pdb=" C   GLY A 121 "
       model="   7" pdb=" N   ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.329  1.420 -0.091 1.40e-02 5.10e+03 4.27e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       79.29 -    91.15: 2
       91.15 -   103.00: 60
      103.00 -   114.86: 2836
      114.86 -   126.72: 1138
      126.72 -   138.57: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" CA  VAL A 126 "
        model="   7" pdb=" C   VAL A 126 "
        model="   7" pdb=" N   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     116.20   93.68   22.52 2.00e+00 2.50e-01 1.27e+02
  angle model="   7" pdb=" N   ARG A 127 "
        model="   7" pdb=" CA  ARG A 127 "
        model="   7" pdb=" CB  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     110.50  128.49  -17.99 1.70e+00 3.46e-01 1.12e+02
  angle model="   7" pdb=" C   ILE A  77 "
        model="   7" pdb=" CA  ILE A  77 "
        model="   7" pdb=" HA  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     109.00   79.29   29.71 3.00e+00 1.11e-01 9.81e+01
  angle model="   7" pdb=" C   ALA A 124 "
        model="   7" pdb=" CA  ALA A 124 "
        model="   7" pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     110.50  124.78  -14.28 1.50e+00 4.44e-01 9.06e+01
  angle model="   7" pdb=" C   LYS A 125 "
        model="   7" pdb=" N   VAL A 126 "
        model="   7" pdb=" CA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     121.70  138.57  -16.87 1.80e+00 3.09e-01 8.79e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.76: 928
       21.76 -    43.51: 59
       43.51 -    65.27: 21
       65.27 -    87.02: 7
       87.02 -   108.78: 2
  Dihedral angle restraints: 1017
    sinusoidal: 562
      harmonic: 455
  Sorted by residual:
  dihedral model="   7" pdb=" CA  VAL A 126 "
           model="   7" pdb=" C   VAL A 126 "
           model="   7" pdb=" N   ARG A 127 "
           model="   7" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   71.22  108.78     0      5.00e+00 4.00e-02 4.73e+02
  dihedral model="   7" pdb=" CA  LYS A 125 "
           model="   7" pdb=" C   LYS A 125 "
           model="   7" pdb=" N   VAL A 126 "
           model="   7" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   72.61  107.39     0      5.00e+00 4.00e-02 4.61e+02
  dihedral model="   7" pdb=" CA  ALA A 124 "
           model="   7" pdb=" C   ALA A 124 "
           model="   7" pdb=" N   LYS A 125 "
           model="   7" pdb=" CA  LYS A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   96.32   83.68     0      5.00e+00 4.00e-02 2.80e+02
  ... (remaining 1014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.110: 164
       1.110 -    2.220: 0
       2.220 -    3.330: 0
       3.330 -    4.439: 2
       4.439 -    5.549: 10
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CA  MET A 128 "
            model="   7" pdb=" N   MET A 128 "
            model="   7" pdb=" C   MET A 128 "
            model="   7" pdb=" CB  MET A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.04    5.55 2.00e-01 2.50e+01 7.70e+02
  chirality model="   7" pdb=" CA  LYS A  79 "
            model="   7" pdb=" N   LYS A  79 "
            model="   7" pdb=" C   LYS A  79 "
            model="   7" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.79    5.30 2.00e-01 2.50e+01 7.02e+02
  chirality model="   7" pdb=" CB  ILE A 122 "
            model="   7" pdb=" CA  ILE A 122 "
            model="   7" pdb=" CG1 ILE A 122 "
            model="   7" pdb=" CG2 ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.52    5.16 2.00e-01 2.50e+01 6.66e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  PHE A  67 "   -0.232 2.00e-02 2.50e+03   9.33e-02 2.61e+02
        model="   7" pdb=" CG  PHE A  67 "    0.038 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 PHE A  67 "    0.064 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 PHE A  67 "    0.049 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 PHE A  67 "    0.004 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 PHE A  67 "    0.019 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  PHE A  67 "   -0.050 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 PHE A  67 "    0.121 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 PHE A  67 "    0.075 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 PHE A  67 "   -0.000 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 PHE A  67 "    0.045 2.00e-02 2.50e+03
        model="   7" pdb=" HZ  PHE A  67 "   -0.133 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CA  VAL A 126 "    0.055 2.00e-02 2.50e+03   1.19e-01 1.42e+02
        model="   7" pdb=" C   VAL A 126 "   -0.205 2.00e-02 2.50e+03
        model="   7" pdb=" O   VAL A 126 "    0.087 2.00e-02 2.50e+03
        model="   7" pdb=" N   ARG A 127 "    0.063 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  50 "   -0.143 2.00e-02 2.50e+03   6.16e-02 1.14e+02
        model="   7" pdb=" CG  TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  50 "    0.038 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  50 "   -0.121 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  50 "    0.064 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  50 "    0.050 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 45
        2.00 -     2.65: 2849
        2.65 -     3.30: 6880
        3.30 -     3.95: 8420
        3.95 -     4.60: 12477
  Nonbonded interactions: 30671
  Sorted by model distance:
  nonbonded model="   7" pdb=" HA  LYS A 125 "
            model="   7" pdb=" H   ARG A 127 "
     model   vdw
     1.346 2.270
  nonbonded model="   7" pdb=" HA  ALA A 124 "
            model="   7" pdb=" H   VAL A 126 "
     model   vdw
     1.650 2.270
  nonbonded model="   7" pdb=" HA  ILE A  78 "
            model="   7" pdb=" HA  LEU A  93 "
     model   vdw
     1.670 2.440
  nonbonded model="   7" pdb=" H   LYS A  79 "
            model="   7" pdb="HG22 THR A  92 "
     model   vdw
     1.674 2.270
  nonbonded model="   7" pdb="HG23 ILE A  77 "
            model="   7" pdb="HG13 ILE A  78 "
     model   vdw
     1.695 2.440
  ... (remaining 30666 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 72
        1.23 -     1.42: 400
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" CZ  ARG A  21 "
       model="  11" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.33e+00
  bond model="  11" pdb=" CD2 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.88e+00
  bond model="  11" pdb=" CD2 HIS A 134 "
       model="  11" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.67e+00
  bond model="  11" pdb=" CE1 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.50e+00
  bond model="  11" pdb=" CE1 HIS A 135 "
       model="  11" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.26e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       91.70 -    99.90: 4
       99.90 -   108.10: 581
      108.10 -   116.30: 2419
      116.30 -   124.50: 978
      124.50 -   132.70: 97
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" CA  VAL A 112 "
        model="  11" pdb=" CB  VAL A 112 "
        model="  11" pdb=" CG1 VAL A 112 "
      ideal   model   delta    sigma   weight residual
     110.40  125.22  -14.82 1.70e+00 3.46e-01 7.60e+01
  angle model="  11" pdb=" C   LEU A 107 "
        model="  11" pdb=" N   ILE A 108 "
        model="  11" pdb=" CA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     121.70  132.70  -11.00 1.80e+00 3.09e-01 3.73e+01
  angle model="  11" pdb=" CB  ILE A 108 "
        model="  11" pdb=" CG1 ILE A 108 "
        model="  11" pdb=" CD1 ILE A 108 "
      ideal   model   delta    sigma   weight residual
     113.80  126.03  -12.23 2.10e+00 2.27e-01 3.39e+01
  angle model="  11" pdb=" C   TYR A 111 "
        model="  11" pdb=" CA  TYR A 111 "
        model="  11" pdb=" HA  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     109.00   91.70   17.30 3.00e+00 1.11e-01 3.33e+01
  angle model="  11" pdb=" CA  ASP A 118 "
        model="  11" pdb=" CB  ASP A 118 "
        model="  11" pdb=" CG  ASP A 118 "
      ideal   model   delta    sigma   weight residual
     112.60  118.22   -5.62 1.00e+00 1.00e+00 3.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 935
       16.97 -    33.94: 65
       33.94 -    50.92: 19
       50.92 -    67.89: 7
       67.89 -    84.86: 3
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  11" pdb=" CA  HIS A 135 "
           model="  11" pdb=" C   HIS A 135 "
           model="  11" pdb=" N   HIS A 136 "
           model="  11" pdb=" CA  HIS A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.67   31.33     0      5.00e+00 4.00e-02 3.93e+01
  dihedral model="  11" pdb=" C   VAL A 104 "
           model="  11" pdb=" N   VAL A 104 "
           model="  11" pdb=" CA  VAL A 104 "
           model="  11" pdb=" CB  VAL A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.35   13.35     0      2.50e+00 1.60e-01 2.85e+01
  dihedral model="  11" pdb=" CA  LEU A 119 "
           model="  11" pdb=" C   LEU A 119 "
           model="  11" pdb=" N   GLU A 120 "
           model="  11" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.06   25.94     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.844: 174
       0.844 -    1.688: 0
       1.688 -    2.531: 0
       2.531 -    3.375: 0
       3.375 -    4.218: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  ILE A 108 "
            model="  11" pdb=" N   ILE A 108 "
            model="  11" pdb=" C   ILE A 108 "
            model="  11" pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -1.78    4.22 2.00e-01 2.50e+01 4.45e+02
  chirality model="  11" pdb=" CA  TYR A 111 "
            model="  11" pdb=" N   TYR A 111 "
            model="  11" pdb=" C   TYR A 111 "
            model="  11" pdb=" CB  TYR A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.34    3.85 2.00e-01 2.50e+01 3.71e+02
  chirality model="  11" pdb=" CA  TYR A 105 "
            model="  11" pdb=" N   TYR A 105 "
            model="  11" pdb=" C   TYR A 105 "
            model="  11" pdb=" CB  TYR A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.26e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A 105 "    0.530 2.00e-02 2.50e+03   2.25e-01 1.52e+03
        model="  11" pdb=" CG  TYR A 105 "   -0.008 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A 105 "   -0.107 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A 105 "   -0.112 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A 105 "   -0.069 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A 105 "   -0.066 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A 105 "    0.052 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A 105 "    0.426 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A 105 "   -0.196 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A 105 "   -0.211 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A 105 "   -0.124 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A 105 "   -0.114 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  50 "    0.351 2.00e-02 2.50e+03   1.58e-01 7.45e+02
        model="  11" pdb=" CG  TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  50 "   -0.074 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  50 "   -0.067 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  50 "   -0.054 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  50 "   -0.061 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  50 "    0.332 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  50 "   -0.119 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  50 "   -0.098 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  50 "   -0.096 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  50 "   -0.115 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  PHE A  15 "    0.226 2.00e-02 2.50e+03   1.01e-01 3.04e+02
        model="  11" pdb=" CG  PHE A  15 "    0.010 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 PHE A  15 "   -0.048 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 PHE A  15 "   -0.054 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 PHE A  15 "   -0.023 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 PHE A  15 "   -0.017 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  PHE A  15 "    0.063 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 PHE A  15 "   -0.102 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 PHE A  15 "   -0.121 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 PHE A  15 "   -0.062 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 PHE A  15 "   -0.045 2.00e-02 2.50e+03
        model="  11" pdb=" HZ  PHE A  15 "    0.173 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 221
        2.22 -     2.82: 4620
        2.82 -     3.41: 6279
        3.41 -     4.01: 7738
        4.01 -     4.60: 11530
  Nonbonded interactions: 30388
  Sorted by model distance:
  nonbonded model="  11" pdb="HG23 VAL A  41 "
            model="  11" pdb=" H   HIS A  43 "
     model   vdw
     1.627 2.270
  nonbonded model="  11" pdb="HG22 ILE A 108 "
            model="  11" pdb=" HA  TYR A 111 "
     model   vdw
     1.683 2.440
  nonbonded model="  11" pdb=" OE1 GLU A  24 "
            model="  11" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.774 1.850
  nonbonded model="  11" pdb=" O   ASP A  95 "
            model="  11" pdb=" HG  SER A  98 "
     model   vdw
     1.794 1.850
  nonbonded model="  11" pdb="HG23 VAL A 104 "
            model="  11" pdb="HD13 ILE A 108 "
     model   vdw
     1.815 2.440
  ... (remaining 30383 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  13" pdb=" CB  ILE A  86 "
        model="  13" pdb=" CB  TYR A  89 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 1.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CB  LYS A  79 "
        model="   4" pdb=" CB  ASP A  88 "
        model="   4" pdb=" CB  LEU A  93 "
        model="   4" pdb=" CB  GLU A 123 "
        model="   4" pdb=" CB  LYS A 125 "
        model="   4" pdb=" CB  VAL A 126 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CB  LYS A  79 "
        model="   6" pdb=" CB  SER A  90 "
        model="   6" pdb=" CB  THR A  92 "
        model="   6" pdb=" CB  ILE A 122 "
        model="   6" pdb=" CB  ARG A 127 "
        model="   6" pdb=" CB  MET A 128 "
        model="   6" pdb=" CB  SER A 130 "
        model="   6" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  246

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   0" pdb=" CB  ILE A  51 "
        model="   0" pdb=" CB  THR A  92 "
        model="   0" pdb=" CB  LEU A  93 "
        model="   0" pdb=" CB  SER A  97 "
        model="   0" pdb=" CB  SER A  98 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 1.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 68
        1.23 -     1.42: 404
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" CD2 HIS A 139 "
       model="  13" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.81e+00
  bond model="  13" pdb=" CA  TYR A  89 "
       model="  13" pdb=" C   TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.525  1.579 -0.054 2.10e-02 2.27e+03 6.72e+00
  bond model="  13" pdb=" CD2 HIS A 136 "
       model="  13" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.43e+00
  bond model="  13" pdb=" CZ  ARG A  21 "
       model="  13" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.26e+00
  bond model="  13" pdb=" CD2 HIS A 137 "
       model="  13" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.20e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       93.01 -   101.68: 6
      101.68 -   110.36: 2207
      110.36 -   119.03: 990
      119.03 -   127.70: 865
      127.70 -   136.37: 11
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" CA  TYR A  89 "
        model="  13" pdb=" CB  TYR A  89 "
        model="  13" pdb=" CG  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     113.90  136.37  -22.47 1.80e+00 3.09e-01 1.56e+02
  angle model="  13" pdb=" C   TYR A  89 "
        model="  13" pdb=" CA  TYR A  89 "
        model="  13" pdb=" CB  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.10  126.55  -16.45 1.90e+00 2.77e-01 7.50e+01
  angle model="  13" pdb=" CA  ASP A 103 "
        model="  13" pdb=" CB  ASP A 103 "
        model="  13" pdb=" CG  ASP A 103 "
      ideal   model   delta    sigma   weight residual
     112.60  120.65   -8.05 1.00e+00 1.00e+00 6.48e+01
  angle model="  13" pdb=" C   TYR A  89 "
        model="  13" pdb=" CA  TYR A  89 "
        model="  13" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   93.01   15.99 3.00e+00 1.11e-01 2.84e+01
  angle model="  13" pdb=" CA  ASP A 110 "
        model="  13" pdb=" CB  ASP A 110 "
        model="  13" pdb=" CG  ASP A 110 "
      ideal   model   delta    sigma   weight residual
     112.60  117.72   -5.12 1.00e+00 1.00e+00 2.63e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.88: 969
       24.88 -    49.76: 44
       49.76 -    74.65: 13
       74.65 -    99.53: 2
       99.53 -   124.41: 1
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  13" pdb=" CA  LYS A  85 "
           model="  13" pdb=" C   LYS A  85 "
           model="  13" pdb=" N   ILE A  86 "
           model="  13" pdb=" CA  ILE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   55.59  124.41     0      5.00e+00 4.00e-02 6.19e+02
  dihedral model="  13" pdb=" CA  ASP A  88 "
           model="  13" pdb=" C   ASP A  88 "
           model="  13" pdb=" N   TYR A  89 "
           model="  13" pdb=" CA  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.89  -46.11     0      5.00e+00 4.00e-02 8.51e+01
  dihedral model="  13" pdb=" CA  TYR A  89 "
           model="  13" pdb=" C   TYR A  89 "
           model="  13" pdb=" N   SER A  90 "
           model="  13" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.16  -32.84     0      5.00e+00 4.00e-02 4.31e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.950: 174
       0.950 -    1.900: 0
       1.900 -    2.850: 0
       2.850 -    3.800: 0
       3.800 -    4.750: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  TYR A  89 "
            model="  13" pdb=" N   TYR A  89 "
            model="  13" pdb=" C   TYR A  89 "
            model="  13" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.24    4.75 2.00e-01 2.50e+01 5.64e+02
  chirality model="  13" pdb=" CA  ILE A  86 "
            model="  13" pdb=" N   ILE A  86 "
            model="  13" pdb=" C   ILE A  86 "
            model="  13" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -1.99    4.42 2.00e-01 2.50e+01 4.89e+02
  chirality model="  13" pdb=" CA  ASP A 103 "
            model="  13" pdb=" N   ASP A 103 "
            model="  13" pdb=" C   ASP A 103 "
            model="  13" pdb=" CB  ASP A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.46e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  89 "   -0.260 2.00e-02 2.50e+03   1.23e-01 4.55e+02
        model="  13" pdb=" CG  TYR A  89 "    0.174 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  89 "    0.035 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  89 "    0.091 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  89 "    0.064 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  89 "    0.009 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  89 "   -0.193 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  89 "   -0.080 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  89 "    0.095 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  89 "    0.120 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  89 "   -0.058 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  50 "    0.226 2.00e-02 2.50e+03   9.70e-02 2.82e+02
        model="  13" pdb=" CG  TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  50 "   -0.052 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  50 "   -0.043 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  50 "   -0.036 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  50 "    0.191 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  50 "   -0.085 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  50 "   -0.059 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  50 "   -0.043 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  50 "   -0.069 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  HIS A  43 "   -0.159 2.00e-02 2.50e+03   9.38e-02 1.76e+02
        model="  13" pdb=" CG  HIS A  43 "    0.124 2.00e-02 2.50e+03
        model="  13" pdb=" ND1 HIS A  43 "    0.127 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 HIS A  43 "    0.029 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 HIS A  43 "   -0.016 2.00e-02 2.50e+03
        model="  13" pdb=" NE2 HIS A  43 "   -0.086 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 HIS A  43 "    0.039 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 HIS A  43 "   -0.060 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.25: 240
        2.25 -     2.84: 4719
        2.84 -     3.43: 5606
        3.43 -     4.01: 6979
        4.01 -     4.60: 10251
  Nonbonded interactions: 27795
  Sorted by model distance:
  nonbonded model="  13" pdb=" HA  TYR A  89 "
            model="  13" pdb=" H   TYR A 105 "
     model   vdw
     1.666 2.270
  nonbonded model="  13" pdb=" OD2 ASP A  36 "
            model="  13" pdb=" HZ1 LYS A  40 "
     model   vdw
     1.702 1.850
  nonbonded model="  13" pdb=" HZ1 LYS A  10 "
            model="  13" pdb=" OD1 ASP A  23 "
     model   vdw
     1.789 1.850
  nonbonded model="  13" pdb=" HD1 TYR A  89 "
            model="  13" pdb=" HB2 TYR A 105 "
     model   vdw
     1.800 2.270
  nonbonded model="  13" pdb=" HD2 TYR A  89 "
            model="  13" pdb=" H   VAL A 104 "
     model   vdw
     1.801 2.100
  ... (remaining 27790 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1105
        1.03 -     1.23: 49
        1.23 -     1.43: 429
        1.43 -     1.62: 651
        1.62 -     1.82: 7
  Bond restraints: 2241
  Sorted by residual:
  bond model="   6" pdb=" N   GLY A  80 "
       model="   6" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.638 -0.187 1.60e-02 3.91e+03 1.37e+02
  bond model="   6" pdb=" C   ARG A 127 "
       model="   6" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.218  0.111 1.40e-02 5.10e+03 6.27e+01
  bond model="   6" pdb=" N   ARG A 127 "
       model="   6" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.601 -0.143 1.90e-02 2.77e+03 5.63e+01
  bond model="   6" pdb=" CA  LYS A  79 "
       model="   6" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.654 -0.129 2.10e-02 2.27e+03 3.78e+01
  bond model="   6" pdb=" CA  ALA A 124 "
       model="   6" pdb=" C   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.525  1.651 -0.126 2.10e-02 2.27e+03 3.61e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       83.87 -    95.75: 7
       95.75 -   107.62: 534
      107.62 -   119.49: 2675
      119.49 -   131.37: 854
      131.37 -   143.24: 7
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   6" pdb=" C   TYR A  91 "
        model="   6" pdb=" N   THR A  92 "
        model="   6" pdb=" CA  THR A  92 "
      ideal   model   delta    sigma   weight residual
     121.70  143.24  -21.54 1.80e+00 3.09e-01 1.43e+02
  angle model="   6" pdb=" C   LYS A 125 "
        model="   6" pdb=" N   VAL A 126 "
        model="   6" pdb=" CA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     121.70  142.77  -21.07 1.80e+00 3.09e-01 1.37e+02
  angle model="   6" pdb=" C   LYS A  79 "
        model="   6" pdb=" N   GLY A  80 "
        model="   6" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  141.70  -20.00 1.80e+00 3.09e-01 1.23e+02
  angle model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" CB  TYR A  89 "
        model="   6" pdb=" CG  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     113.90  132.55  -18.65 1.80e+00 3.09e-01 1.07e+02
  angle model="   6" pdb=" C   ILE A 122 "
        model="   6" pdb=" CA  ILE A 122 "
        model="   6" pdb=" HA  ILE A 122 "
      ideal   model   delta    sigma   weight residual
     109.00   83.87   25.13 3.00e+00 1.11e-01 7.01e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.30: 949
       25.30 -    50.59: 52
       50.59 -    75.89: 5
       75.89 -   101.18: 3
      101.18 -   126.48: 5
  Dihedral angle restraints: 1014
    sinusoidal: 561
      harmonic: 453
  Sorted by residual:
  dihedral model="   6" pdb=" CA  ALA A 124 "
           model="   6" pdb=" C   ALA A 124 "
           model="   6" pdb=" N   LYS A 125 "
           model="   6" pdb=" CA  LYS A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   53.52  126.48     0      5.00e+00 4.00e-02 6.40e+02
  dihedral model="   6" pdb=" CA  ILE A 122 "
           model="   6" pdb=" C   ILE A 122 "
           model="   6" pdb=" N   GLU A 123 "
           model="   6" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   58.45  121.55     0      5.00e+00 4.00e-02 5.91e+02
  dihedral model="   6" pdb=" CA  GLU A 123 "
           model="   6" pdb=" C   GLU A 123 "
           model="   6" pdb=" N   ALA A 124 "
           model="   6" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   61.13  118.87     0      5.00e+00 4.00e-02 5.65e+02
  ... (remaining 1011 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.114: 165
       1.114 -    2.226: 0
       2.226 -    3.339: 0
       3.339 -    4.452: 3
       4.45  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 68
        1.23 -     1.43: 407
        1.43 -     1.62: 657
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   4" pdb=" N   GLU A 123 "
       model="   4" pdb=" CA  GLU A 123 "
    ideal  model  delta    sigma   weight residual
    1.458  1.330  0.128 1.90e-02 2.77e+03 4.53e+01
  bond model="   4" pdb=" CB  LEU A  93 "
       model="   4" pdb=" CG  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.611 -0.081 2.00e-02 2.50e+03 1.63e+01
  bond model="   4" pdb=" CA  ASP A  88 "
       model="   4" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.608 -0.083 2.10e-02 2.27e+03 1.56e+01
  bond model="   4" pdb=" CA  LYS A 125 "
       model="   4" pdb=" C   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.525  1.448  0.077 2.10e-02 2.27e+03 1.35e+01
  bond model="   4" pdb=" C   GLU A 123 "
       model="   4" pdb=" N   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.329  1.284  0.045 1.40e-02 5.10e+03 1.04e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       76.73 -    91.33: 9
       91.33 -   105.93: 193
      105.93 -   120.53: 3302
      120.53 -   135.13: 568
      135.13 -   149.74: 7
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   4" pdb=" N   LEU A  93 "
        model="   4" pdb=" CA  LEU A  93 "
        model="   4" pdb=" C   LEU A  93 "
      ideal   model   delta    sigma   weight residual
     111.00  149.74  -38.74 2.80e+00 1.28e-01 1.91e+02
  angle model="   4" pdb=" CB  LEU A  93 "
        model="   4" pdb=" CA  LEU A  93 "
        model="   4" pdb=" HA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     109.00  148.51  -39.51 3.00e+00 1.11e-01 1.73e+02
  angle model="   4" pdb=" CA  VAL A 126 "
        model="   4" pdb=" CB  VAL A 126 "
        model="   4" pdb=" CG1 VAL A 126 "
      ideal   model   delta    sigma   weight residual
     110.40  132.21  -21.81 1.70e+00 3.46e-01 1.65e+02
  angle model="   4" pdb=" CB  THR A  92 "
        model="   4" pdb=" CA  THR A  92 "
        model="   4" pdb=" HA  THR A  92 "
      ideal   model   delta    sigma   weight residual
     109.00  143.12  -34.12 3.00e+00 1.11e-01 1.29e+02
  angle model="   4" pdb=" CA  VAL A 126 "
        model="   4" pdb=" CB  VAL A 126 "
        model="   4" pdb=" HB  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     109.00   76.73   32.27 3.00e+00 1.11e-01 1.16e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.58: 930
       22.58 -    45.16: 67
       45.16 -    67.74: 13
       67.74 -    90.32: 4
       90.32 -   112.89: 3
  Dihedral angle restraints: 1017
    sinusoidal: 562
      harmonic: 455
  Sorted by residual:
  dihedral model="   4" pdb=" CA  TYR A  89 "
           model="   4" pdb=" C   TYR A  89 "
           model="   4" pdb=" N   SER A  90 "
           model="   4" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -67.11 -112.89     0      5.00e+00 4.00e-02 5.10e+02
  dihedral model="   4" pdb=" CA  ILE A  77 "
           model="   4" pdb=" C   ILE A  77 "
           model="   4" pdb=" N   ILE A  78 "
           model="   4" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   68.33  111.67     0      5.00e+00 4.00e-02 4.99e+02
  dihedral model="   4" pdb=" CA  LYS A 125 "
           model="   4" pdb=" C   LYS A 125 "
           model="   4" pdb=" N   VAL A 126 "
           model="   4" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  -79.48 -100.52     0      5.00e+00 4.00e-02 4.04e+02
  ... (remaining 1014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.140: 163
       1.140 -    2.280: 2
       2.280 -    3.421: 1
       3.421 -    4.561: 2
       4.561 -    5.701: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CA  LYS A  79 "
            model="   4" pdb=" N   LYS A  79 "
            model="   4" pdb=" C   LYS A  79 "
            model="   4" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.19    5.70 2.00e-01 2.50e+01 8.12e+02
  chirality model="   4" pdb=" CB  ILE A 122 "
            model="   4" pdb=" CA  ILE A 122 "
            model="   4" pdb=" CG1 ILE A 122 "
            model="   4" pdb=" CG2 ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.48    5.13 2.00e-01 2.50e+01 6.58e+02
  chirality model="   4" pdb=" CB  ILE A  77 "
            model="   4" pdb=" CA  ILE A  77 "
            model="   4" pdb=" CG1 ILE A  77 "
            model="   4" pdb=" CG2 ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.40    5.05 2.00e-01 2.50e+01 6.37e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  91 "   -0.237 2.00e-02 2.50e+03   9.25e-02 2.57e+02
        model="   4" pdb=" CG  TYR A  91 "    0.040 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  91 "    0.066 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  91 "    0.047 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  91 "    0.025 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  91 "   -0.014 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  91 "   -0.120 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  91 "    0.127 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  91 "    0.067 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  91 "   -0.035 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  91 "    0.036 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  89 "    0.130 2.00e-02 2.50e+03   5.20e-02 8.10e+01
        model="   4" pdb=" CG  TYR A  89 "   -0.067 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  89 "   -0.038 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  89 "   -0.026 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  89 "   -0.018 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  89 "    0.076 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  89 "   -0.043 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  89 "    0.018 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  89 "   -0.024 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  12 "   -0.100 2.00e-02 2.50e+03   4.56e-02 6.25e+01
        model="   4" pdb=" CG  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  12 "    0.026 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  12 "   -0.094 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  12 "    0.048 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  12 "    0.043 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.40 -     2.04: 83
        2.04 -     2.68: 3310
   2 -    5.565: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CA  LYS A  79 "
            model="   6" pdb=" N   LYS A  79 "
            model="   6" pdb=" C   LYS A  79 "
            model="   6" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.05    5.56 2.00e-01 2.50e+01 7.74e+02
  chirality model="   6" pdb=" CB  ILE A  78 "
            model="   6" pdb=" CA  ILE A  78 "
            model="   6" pdb=" CG1 ILE A  78 "
            model="   6" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.48    5.13 2.00e-01 2.50e+01 6.57e+02
  chirality model="   6" pdb=" CA  ARG A 127 "
            model="   6" pdb=" N   ARG A 127 "
            model="   6" pdb=" C   ARG A 127 "
            model="   6" pdb=" CB  ARG A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.43    4.94 2.00e-01 2.50e+01 6.11e+02
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  12 "    0.141 2.00e-02 2.50e+03   6.32e-02 1.20e+02
        model="   6" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  12 "   -0.029 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  12 "   -0.023 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  12 "    0.132 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  12 "   -0.047 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  12 "   -0.049 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  12 "   -0.040 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  12 "   -0.038 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A 111 "    0.114 2.00e-02 2.50e+03   4.59e-02 6.32e+01
        model="   6" pdb=" CG  TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A 111 "   -0.026 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A 111 "    0.082 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A 111 "   -0.035 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A 111 "   -0.041 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CA  VAL A 126 "   -0.030 2.00e-02 2.50e+03   6.09e-02 3.71e+01
        model="   6" pdb=" C   VAL A 126 "    0.105 2.00e-02 2.50e+03
        model="   6" pdb=" O   VAL A 126 "   -0.042 2.00e-02 2.50e+03
        model="   6" pdb=" N   ARG A 127 "   -0.033 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.40 -     2.04: 58
        2.04 -     2.68: 3180
        2.68 -     3.32: 6685
        3.32 -     3.96: 8004
        3.96 -     4.60: 12079
  Nonbonded interactions: 30006
  Sorted by model distance:
  nonbonded model="   6" pdb=" HB3 TYR A  89 "
            model="   6" pdb=" HA  GLN A 100 "
     model   vdw
     1.401 2.440
  nonbonded model="   6" pdb=" HA  ALA A 124 "
            model="   6" pdb=" H   VAL A 126 "
     model   vdw
     1.529 2.270
  nonbonded model="   6" pdb="HG23 ILE A  71 "
            model="   6" pdb="HD11 ILE A  78 "
     model   vdw
     1.629 2.440
  nonbonded model="   6" pdb=" HG  LEU A  93 "
            model="   6" pdb=" H   ASP A  95 "
     model   vdw
     1.698 2.270
  nonbonded model="   6" pdb=" OD1 ASP A  95 "
            model="   6" pdb=" HG  SER A  97 "
     model   vdw
     1.745 1.850
  ... (remaining 30001 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
     2.68 -     3.32: 6995
        3.32 -     3.96: 8823
        3.96 -     4.60: 12974
  Nonbonded interactions: 32185
  Sorted by model distance:
  nonbonded model="   4" pdb="HD13 LEU A  93 "
            model="   4" pdb=" H   ASP A  95 "
     model   vdw
     1.404 2.270
  nonbonded model="   4" pdb=" H   GLU A 123 "
            model="   4" pdb="HG22 VAL A 126 "
     model   vdw
     1.417 2.270
  nonbonded model="   4" pdb=" HA  VAL A 126 "
            model="   4" pdb=" H   ARG A 129 "
     model   vdw
     1.451 2.270
  nonbonded model="   4" pdb=" HB  VAL A 126 "
            model="   4" pdb=" H   MET A 128 "
     model   vdw
     1.579 2.270
  nonbonded model="   4" pdb=" HB2 GLU A 123 "
            model="   4" pdb=" H   LYS A 125 "
     model   vdw
     1.611 2.270
  ... (remaining 32180 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 68
        1.23 -     1.43: 404
        1.43 -     1.62: 659
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CA  ILE A  78 "
       model="   0" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.644 -0.119 2.10e-02 2.27e+03 3.23e+01
  bond model="   0" pdb=" N   GLY A  80 "
       model="   0" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.539 -0.088 1.60e-02 3.91e+03 3.04e+01
  bond model="   0" pdb=" N   LYS A  79 "
       model="   0" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.554 -0.096 1.90e-02 2.77e+03 2.53e+01
  bond model="   0" pdb=" CA  ASP A  88 "
       model="   0" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.612 -0.087 2.10e-02 2.27e+03 1.71e+01
  bond model="   0" pdb=" C   ILE A  78 "
       model="   0" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.386 -0.057 1.40e-02 5.10e+03 1.68e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       91.54 -   100.39: 18
      100.39 -   109.24: 1129
      109.24 -   118.09: 1949
      118.09 -   126.94: 958
      126.94 -   135.79: 25
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  79 "
        model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  135.79  -14.09 1.80e+00 3.09e-01 6.13e+01
  angle model="   0" pdb=" C   ILE A  78 "
        model="   0" pdb=" N   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  135.62  -13.92 1.80e+00 3.09e-01 5.98e+01
  angle model="   0" pdb=" C   ASP A  88 "
        model="   0" pdb=" N   TYR A  89 "
        model="   0" pdb=" CA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     121.70  135.44  -13.74 1.80e+00 3.09e-01 5.83e+01
  angle model="   0" pdb=" C   TYR A  89 "
        model="   0" pdb=" CA  TYR A  89 "
        model="   0" pdb=" CB  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.10  124.45  -14.35 1.90e+00 2.77e-01 5.70e+01
  angle model="   0" pdb=" O   LEU A  93 "
        model="   0" pdb=" C   LEU A  93 "
        model="   0" pdb=" N   GLY A  94 "
      ideal   model   delta    sigma   weight residual
     123.00  111.08   11.92 1.60e+00 3.91e-01 5.55e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.48: 930
       18.48 -    36.96: 60
       36.96 -    55.44: 24
       55.44 -    73.92: 5
       73.92 -    92.40: 4
  Dihedral angle restraints: 1023
    sinusoidal: 562
      harmonic: 461
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  94 "
           model="   0" pdb=" C   GLY A  94 "
           model="   0" pdb=" N   ASP A  95 "
           model="   0" pdb=" CA  ASP A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   87.60   92.40     0      5.00e+00 4.00e-02 3.42e+02
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   94.95   85.05     0      5.00e+00 4.00e-02 2.89e+02
  dihedral model="   0" pdb=" CA  SER A  97 "
           model="   0" pdb=" C   SER A  97 "
           model="   0" pdb=" N   SER A  98 "
           model="   0" pdb=" CA  SER A  98 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   95.39   84.61     0      5.00e+00 4.00e-02 2.86e+02
  ... (remaining 1020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.076: 171
       1.076 -    2.151: 0
       2.151 -    3.226: 0
       3.226 -    4.302: 0
       4.302 -    5.377: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  THR A  92 "
            model="   0" pdb=" N   THR A  92 "
            model="   0" pdb=" C   THR A  92 "
            model="   0" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.85    5.38 2.00e-01 2.50e+01 7.23e+02
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.59    5.10 2.00e-01 2.50e+01 6.49e+02
  chirality model="   0" pdb=" CA  SER A  98 "
            model="   0" pdb=" N   SER A  98 "
            model="   0" pdb=" C   SER A  98 "
            model="   0" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.40    4.91 2.00e-01 2.50e+01 6.03e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "   -0.311 2.00e-02 2.50e+03   1.19e-01 4.26e+02
        model="   0" pdb=" CG  PHE A  15 "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "    0.087 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "   -0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "    0.111 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "    0.159 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "   -0.121 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.187 2.00e-02 2.50e+03   7.60e-02 1.73e+02
        model="   0" pdb=" CG  TYR A  89 "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.065 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.128 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.070 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.092 2.00e-02 2.50e+03   5.66e-02 9.59e+01
        model="   0" pdb=" CG  TYR A  91 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.118 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.048 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 241
        2.23 -     2.83: 4723
        2.83 -     3.42: 6245
        3.42 -     4.01: 7761
        4.01 -     4.60: 11535
  Nonbonded interactions: 30505
  Sorted by model distance:
  nonbonded model="   0" pdb=" H   LYS A  79 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.643 2.100
  nonbonded model="   0" pdb=" HA  LYS A  79 "
            model="   0" pdb=" HB  THR A  92 "
     model   vdw
     1.736 2.440
  nonbonded model="   0" pdb=" HB  ILE A  78 "
            model="   0" pdb=" H   TYR A  81 "
     model   vdw
     1.800 2.270
  nonbonded model="   0" pdb=" HB  THR A  92 "
            model="   0" pdb=" H   LEU A  93 "
     model   vdw
     1.800 2.270
  nonbonded model="   0" pdb=" HA  LEU A 132 "
            model="   0" pdb=" H   GLU A 133 "
     model   vdw
     1.819 2.270
  ... (remaining 30500 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  14" pdb=" CB  ASN A  72 "
        model="  14" pdb=" CB  LYS A  85 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.52
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.59 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 81
        1.23 -     1.42: 391
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" CZ  ARG A  21 "
       model="  11" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.33e+00
  bond model="  11" pdb=" CD2 HIS A 136 "
       model="  11" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.20e+00
  bond model="  11" pdb=" CD2 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.07e+00
  bond model="  11" pdb=" CD2 HIS A 138 "
       model="  11" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.28e+00
  bond model="  11" pdb=" CE1 HIS A  43 "
       model="  11" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.92e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.10 -   105.92: 127
      105.92 -   111.73: 2411
      111.73 -   117.55: 528
      117.55 -   123.36: 821
      123.36 -   129.17: 192
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" CA  MET A   1 "
        model="  11" pdb=" C   MET A   1 "
        model="  11" pdb=" N   LEU A   2 "
      ideal   model   delta    sigma   weight residual
     116.20  125.42   -9.22 2.00e+00 2.50e-01 2.12e+01
  angle model="  11" pdb=" OE1 GLN A  66 "
        model="  11" pdb=" CD  GLN A  66 "
        model="  11" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.15    4.45 1.00e+00 1.00e+00 1.98e+01
  angle model="  11" pdb=" CB  HIS A  43 "
        model="  11" pdb=" CG  HIS A  43 "
        model="  11" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  125.62    5.58 1.30e+00 5.92e-01 1.84e+01
  angle model="  11" pdb=" O   MET A   1 "
        model="  11" pdb=" C   MET A   1 "
        model="  11" pdb=" N   LEU A   2 "
      ideal   model   delta    sigma   weight residual
     123.00  116.34    6.66 1.60e+00 3.91e-01 1.73e+01
  angle model="  11" pdb=" CA  TYR A  89 "
        model="  11" pdb=" CB  TYR A  89 "
        model="  11" pdb=" CG  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     113.90  121.36   -7.46 1.80e+00 3.09e-01 1.72e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 898
       17.32 -    34.63: 84
       34.63 -    51.95: 35
       51.95 -    69.26: 11
       69.26 -    86.58: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  11" pdb=" CA  MET A   1 "
           model="  11" pdb=" C   MET A   1 "
           model="  11" pdb=" N   LEU A   2 "
           model="  11" pdb=" CA  LEU A   2 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   39.95  -39.95     0      5.00e+00 4.00e-02 6.38e+01
  dihedral model="  11" pdb=" CA  PRO A 114 "
           model="  11" pdb=" C   PRO A 114 "
           model="  11" pdb=" N   ALA A 115 "
           model="  11" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.49   22.51     0      5.00e+00 4.00e-02 2.03e+01
  dihedral model="  11" pdb=" CA  ALA A 115 "
           model="  11" pdb=" C   ALA A 115 "
           model="  11" pdb=" N   ASP A 116 "
           model="  11" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.74  -19.26     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 77
       0.050 -    0.100: 48
       0.100 -    0.151: 29
       0.151 -    0.201: 16
       0.201 -    0.251: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  VAL A 112 "
            model="  11" pdb=" N   VAL A 112 "
            model="  11" pdb=" C   VAL A 112 "
            model="  11" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality model="  11" pdb=" CA  ASP A  44 "
            model="  11" pdb=" N   ASP A  44 "
            model="  11" pdb=" C   ASP A  44 "
            model="  11" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="  11" pdb=" CG  LEU A  53 "
            model="  11" pdb=" CB  LEU A  53 "
            model="  11" pdb=" CD1 LEU A  53 "
            model="  11" pdb=" CD2 LEU A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A 111 "    0.212 2.00e-02 2.50e+03   8.02e-02 1.93e+02
        model="  11" pdb=" CG  TYR A 111 "   -0.037 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A 111 "   -0.050 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A 111 "   -0.050 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A 111 "    0.102 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A 111 "   -0.086 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A 111 "   -0.086 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  89 "    0.121 2.00e-02 2.50e+03   7.50e-02 1.69e+02
        model="  11" pdb=" CG  TYR A  89 "    0.016 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  89 "   -0.057 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  89 "    0.032 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  89 "   -0.029 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  89 "    0.038 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  89 "    0.041 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  89 "   -0.168 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  89 "    0.086 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  89 "   -0.093 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  PHE A  45 "   -0.056 2.00e-02 2.50e+03   6.00e-02 1.08e+02
        model="  11" pdb=" CG  PHE A  45 "   -0.043 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 PHE A  45 "   -0.016 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 PHE A  45 "    0.036 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 PHE A  45 "    0.036 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 PHE A  45 "   -0.017 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  PHE A  45 "   -0.024 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 PHE A  45 "   -0.032 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 PHE A  45 "    0.122 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 PHE A  45 "    0.109 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 PHE A  45 "   -0.046 2.00e-02 2.50e+03
        model="  11" pdb=" HZ  PHE A  45 "   -0.068 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.35: 596
        2.35 -     2.92: 5091
        2.92 -     3.48: 5361
        3.48 -     4.04: 6829
        4.04 -     4.60: 9974
  Nonbonded interactions: 27851
  Sorted by model distance:
  nonbonded model="  11" pdb=" HZ1 LYS A  10 "
            model="  11" pdb=" OD1 ASP A  23 "
     model   vdw
     1.792 1.850
  nonbonded model="  11" pdb="HD22 LEU A   3 "
            model="  11" pdb="HD13 LEU A  53 "
     model   vdw
     1.798 2.440
  nonbonded model="  11" pdb=" OE2 GLU A  24 "
            model="  11" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.811 1.850
  nonbonded model="  11" pdb=" OD1 ASP A  44 "
            model="  11" pdb=" HG  SER A  46 "
     model   vdw
     1.822 1.850
  nonbonded model="  11" pdb=" O   ILE A  30 "
            model="  11" pdb=" HG1 THR A  34 "
     model   vdw
     1.860 1.850
  ... (remaining 27846 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ILE A  78 "
        model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CB  TYR A  89 "
        model="   2" pdb=" CB  SER A  90 "
        model="   2" pdb=" CB  THR A  92 "
        model="   2" pdb=" CB  LEU A  93 "
        model="   2" pdb=" CB  SER A  98 "
        model="   2" pdb=" CB  ASP A 116 "
        model="   2" pdb=" CB  MET A 128 "
        model="   2" pdb=" CB  SER A 130 "
        model="   2" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  240

  Time building geometry restraints manager: 1.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.21
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.32 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  TYR A  89 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 1.29 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 105
        1.23 -     1.43: 367
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" CZ  ARG A 129 "
       model="  14" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.87e+00
  bond model="  14" pdb=" CZ  ARG A  21 "
       model="  14" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.76e+00
  bond model="  14" pdb=" CD2 HIS A 139 "
       model="  14" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.71e+00
  bond model="  14" pdb=" CZ  ARG A 127 "
       model="  14" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.54e+00
  bond model="  14" pdb=" CD2 HIS A 137 "
       model="  14" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.37e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       93.21 -   101.06: 11
      101.06 -   108.92: 879
      108.92 -   116.78: 2130
      116.78 -   124.64: 962
      124.64 -   132.50: 97
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" N   THR A  83 "
        model="  14" pdb=" CA  THR A  83 "
        model="  14" pdb=" CB  THR A  83 "
      ideal   model   delta    sigma   weight residual
     111.50  100.98   10.52 1.70e+00 3.46e-01 3.83e+01
  angle model="  14" pdb=" C   GLU A  84 "
        model="  14" pdb=" N   LYS A  85 "
        model="  14" pdb=" CA  LYS A  85 "
      ideal   model   delta    sigma   weight residual
     121.70  132.50  -10.80 1.80e+00 3.09e-01 3.60e+01
  angle model="  14" pdb=" C   ILE A  71 "
        model="  14" pdb=" N   ASN A  72 "
        model="  14" pdb=" CA  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     121.70  132.30  -10.60 1.80e+00 3.09e-01 3.47e+01
  angle model="  14" pdb=" C   LYS A  85 "
        model="  14" pdb=" CA  LYS A  85 "
        model="  14" pdb=" HA  LYS A  85 "
      ideal   model   delta    sigma   weight residual
     109.00   93.21   15.79 3.00e+00 1.11e-01 2.77e+01
  angle model="  14" pdb=" C   ASN A  72 "
        model="  14" pdb=" CA  ASN A  72 "
        model="  14" pdb=" HA  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     109.00   93.22   15.78 3.00e+00 1.11e-01 2.77e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.61: 947
       21.61 -    43.22: 64
       43.22 -    64.83: 15
       64.83 -    86.45: 2
       86.45 -   108.06: 1
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  14" pdb=" CA  GLY A  73 "
           model="  14" pdb=" C   GLY A  73 "
           model="  14" pdb=" N   ASP A  74 "
           model="  14" pdb=" CA  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -71.94 -108.06     0      5.00e+00 4.00e-02 4.67e+02
  dihedral model="  14" pdb=" CA  ILE A  71 "
           model="  14" pdb=" C   ILE A  71 "
           model="  14" pdb=" N   ASN A  72 "
           model="  14" pdb=" CA  ASN A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -129.02  -50.98     0      5.00e+00 4.00e-02 1.04e+02
  dihedral model="  14" pdb=" CA  ASP A  88 "
           model="  14" pdb=" C   ASP A  88 "
           model="  14" pdb=" N   TYR A  89 "
           model="  14" pdb=" CA  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.08  -48.92     0      5.00e+00 4.00e-02 9.57e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.828: 174
       0.828 -    1.656: 0
       1.656 -    2.484: 0
       2.484 -    3.312: 0
       3.312 -    4.140: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CA  ASN A  72 "
            model="  14" pdb=" N   ASN A  72 "
            model="  14" pdb=" C   ASN A  72 "
            model="  14" pdb=" CB  ASN A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.63    4.14 2.00e-01 2.50e+01 4.28e+02
  chirality model="  14" pdb=" CA  LYS A  85 "
            model="  14" pdb=" N   LYS A  85 "
            model="  14" pdb=" C   LYS A  85 "
            model="  14" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.59    4.10 2.00e-01 2.50e+01 4.20e+02
  chirality model="  14" pdb=" CA  ASP A  74 "
            model="  14" pdb=" N   ASP A  74 "
            model="  14" pdb=" C   ASP A  74 "
            model="  14" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.20e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  89 "   -0.878 2.00e-02 2.50e+03   3.62e-01 3.93e+03
        model="  14" pdb=" CG  TYR A  89 "   -0.020 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  89 "    0.186 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  89 "    0.170 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  89 "    0.085 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  89 "    0.105 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  89 "   -0.112 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  89 "   -0.614 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  89 "    0.389 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  89 "    0.338 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  89 "    0.146 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  89 "    0.204 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A 111 "    0.182 2.00e-02 2.50e+03   7.02e-02 1.48e+02
        model="  14" pdb=" CG  TYR A 111 "   -0.069 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A 111 "   -0.041 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A 111 "   -0.056 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A 111 "    0.030 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A 111 "   -0.048 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A 111 "   -0.094 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A 111 "    0.060 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  HIS A 136 "   -0.125 2.00e-02 2.50e+03   7.34e-02 1.08e+02
        model="  14" pdb=" CG  HIS A 136 "    0.107 2.00e-02 2.50e+03
        model="  14" pdb=" ND1 HIS A 136 "    0.097 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 HIS A 136 "    0.023 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 HIS A 136 "   -0.012 2.00e-02 2.50e+03
        model="  14" pdb=" NE2 HIS A 136 "   -0.052 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 HIS A 136 "    0.017 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 HIS A 136 "   -0.055 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 217
        2.21 -     2.81: 4465
        2.81 -     3.41: 6159
        3.41 -     4.00: 7504
        4.00 -     4.60: 10987
  Nonbonded interactions: 29332
  Sorted by model distance:
  nonbonded model="  14" pdb="HG11 VAL A 112 "
            model="  14" pdb=" HB3 MET A 128 "
     model   vdw
     1.615 2.440
  nonbonded model="  14" pdb=" HB3 ASP A  74 "
            model="  14" pdb=" H   SER A  76 "
     model   vdw
     1.687 2.270
  nonbonded model="  14" pdb=" HZ1 LYS A  10 "
            model="  14" pdb=" OD1 ASP A  23 "
     model   vdw
     1.719 1.850
  nonbonded model="  14" pdb=" OE1 GLU A  75 "
            model="  14" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.723 1.850
  nonbonded model="  14" pdb=" HG1 THR A  56 "
            model="  14" pdb=" HE2 TYR A 111 "
     model   vdw
     1.750 2.100
  ... (remaining 29327 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 58
        1.23 -     1.43: 417
        1.43 -     1.62: 657
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" N   MET A 128 "
       model="   2" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.552 -0.094 1.90e-02 2.77e+03 2.44e+01
  bond model="   2" pdb=" N   GLY A  80 "
       model="   2" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.523 -0.072 1.60e-02 3.91e+03 2.01e+01
  bond model="   2" pdb=" C   ARG A 127 "
       model="   2" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.384 -0.055 1.40e-02 5.10e+03 1.56e+01
  bond model="   2" pdb=" CA  LYS A  79 "
       model="   2" pdb=" CB  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.530  1.606 -0.076 2.00e-02 2.50e+03 1.46e+01
  bond model="   2" pdb=" C   VAL A 126 "
       model="   2" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.282  0.047 1.40e-02 5.10e+03 1.11e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       91.16 -   100.41: 19
      100.41 -   109.65: 1994
      109.65 -   118.90: 1151
      118.90 -   128.14: 892
      128.14 -   137.39: 23
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CG  LYS A  79 "
        model="   2" pdb=" CD  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     111.30  137.39  -26.09 2.30e+00 1.89e-01 1.29e+02
  angle model="   2" pdb=" C   VAL A 126 "
        model="   2" pdb=" N   ARG A 127 "
        model="   2" pdb=" CA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     121.70  107.64   14.06 1.80e+00 3.09e-01 6.10e+01
  angle model="   2" pdb=" C   TYR A  91 "
        model="   2" pdb=" N   THR A  92 "
        model="   2" pdb=" CA  THR A  92 "
      ideal   model   delta    sigma   weight residual
     121.70  135.41  -13.71 1.80e+00 3.09e-01 5.80e+01
  angle model="   2" pdb=" C   SER A  97 "
        model="   2" pdb=" N   SER A  98 "
        model="   2" pdb=" CA  SER A  98 "
      ideal   model   delta    sigma   weight residual
     121.70  133.92  -12.22 1.80e+00 3.09e-01 4.61e+01
  angle model="   2" pdb=" C   ASP A 118 "
        model="   2" pdb=" N   LEU A 119 "
        model="   2" pdb=" CA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     121.70  133.44  -11.74 1.80e+00 3.09e-01 4.26e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.92: 935
       24.92 -    49.84: 46
       49.84 -    74.76: 21
       74.76 -    99.68: 5
       99.68 -   124.60: 2
  Dihedral angle restraints: 1009
    sinusoidal: 562
      harmonic: 447
  Sorted by residual:
  dihedral model="   2" pdb=" CA  GLY A  96 "
           model="   2" pdb=" C   GLY A  96 "
           model="   2" pdb=" N   SER A  97 "
           model="   2" pdb=" CA  SER A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   55.40  124.60     0      5.00e+00 4.00e-02 6.21e+02
  dihedral model="   2" pdb=" CA  VAL A 126 "
           model="   2" pdb=" C   VAL A 126 "
           model="   2" pdb=" N   ARG A 127 "
           model="   2" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   67.83  112.17     0      5.00e+00 4.00e-02 5.03e+02
  dihedral model="   2" pdb=" CA  SER A  90 "
           model="   2" pdb=" C   SER A  90 "
           model="   2" pdb=" N   TYR A  91 "
           model="   2" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   90.13   89.87     0      5.00e+00 4.00e-02 3.23e+02
  ... (remaining 1006 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.096: 161
       1.096 -    2.191: 0
       2.191 -    3.287: 0
       3.287 -    4.382: 1
       4.382 -    5.477: 14
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CA  THR A  92 "
            model="   2" pdb=" N   THR A  92 "
            model="   2" pdb=" C   THR A  92 "
            model="   2" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.95    5.48 2.00e-01 2.50e+01 7.50e+02
  chirality model="   2" pdb=" CA  SER A  98 "
            model="   2" pdb=" N   SER A  98 "
            model="   2" pdb=" C   SER A  98 "
            model="   2" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.92    5.43 2.00e-01 2.50e+01 7.37e+02
  chirality model="   2" pdb=" CA  LYS A  79 "
            model="   2" pdb=" N   LYS A  79 "
            model="   2" pdb=" C   LYS A  79 "
            model="   2" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.89    5.40 2.00e-01 2.50e+01 7.30e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  91 "    0.244 2.00e-02 2.50e+03   9.86e-02 2.91e+02
        model="   2" pdb=" CG  TYR A  91 "   -0.071 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  91 "   -0.070 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  91 "   -0.043 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  91 "   -0.040 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  91 "    0.160 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  91 "   -0.110 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  91 "   -0.026 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  91 "    0.026 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  91 "   -0.067 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A 111 "    0.117 2.00e-02 2.50e+03   4.67e-02 6.55e+01
        model="   2" pdb=" CG  TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A 111 "   -0.027 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A 111 "   -0.025 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A 111 "    0.080 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A 111 "   -0.044 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A 111 "   -0.037 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A 111 "   -0.020 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  12 "   -0.099 2.00e-02 2.50e+03   4.41e-02 5.83e+01
        model="   2" pdb=" CG  TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  12 "    0.026 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  12 "   -0.089 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  12 "    0.046 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  12 "    0.039 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 397
        2.30 -     2.87: 5131
        2.87 -     3.45: 5799
        3.45 -     4.02: 7475
        4.02 -     4.60: 11078
  Nonbonded interactions: 29880
  Sorted by model distance:
  nonbonded model="   2" pdb=" HA2 GLY A  96 "
            model="   2" pdb=" H   SER A  98 "
     model   vdw
     1.720 2.270
  nonbonded model="   2" pdb=" OD2 ASP A  36 "
            model="   2" pdb=" HH  TYR A  68 "
     model   vdw
     1.780 1.850
  nonbonded model="   2" pdb=" OD2 ASP A  44 "
            model="   2" pdb=" HG  SER A  46 "
     model   vdw
     1.791 1.850
  nonbonded model="   2" pdb=" HA  SER A  76 "
            model="   2" pdb=" HD2 LYS A  79 "
     model   vdw
     1.804 2.440
  nonbonded model="   2" pdb=" OD1 ASP A  74 "
            model="   2" pdb=" HG  SER A  76 "
     model   vdw
     1.805 1.850
  ... (remaining 29875 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 56
        1.23 -     1.43: 416
        1.43 -     1.62: 654
        1.62 -     1.82: 10
  Bond restraints: 2242
  Sorted by residual:
  bond model="   4" pdb=" N   LEU A 132 "
       model="   4" pdb=" CA  LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.458  1.679 -0.221 1.90e-02 2.77e+03 1.35e+02
  bond model="   4" pdb=" N   ILE A 122 "
       model="   4" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.665 -0.207 1.90e-02 2.77e+03 1.19e+02
  bond model="   4" pdb=" N   MET A 128 "
       model="   4" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.650 -0.192 1.90e-02 2.77e+03 1.02e+02
  bond model="   4" pdb=" CA  GLY A 121 "
       model="   4" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.692 -0.176 1.80e-02 3.09e+03 9.55e+01
  bond model="   4" pdb=" N   VAL A 126 "
       model="   4" pdb=" CA  VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.640 -0.182 1.90e-02 2.77e+03 9.18e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       77.05 -    91.85: 9
       91.85 -   106.65: 252
      106.65 -   121.45: 3352
      121.45 -   136.25: 463
      136.25 -   151.05: 3
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   4" pdb=" C   ILE A 122 "
        model="   4" pdb=" CA  ILE A 122 "
        model="   4" pdb=" CB  ILE A 122 "
      ideal   model   delta    sigma   weight residual
     111.60  146.09  -34.49 2.00e+00 2.50e-01 2.97e+02
  angle model="   4" pdb=" N   ILE A 122 "
        model="   4" pdb=" CA  ILE A 122 "
        model="   4" pdb=" CB  ILE A 122 "
      ideal   model   delta    sigma   weight residual
     111.50   85.52   25.98 1.70e+00 3.46e-01 2.34e+02
  angle model="   4" pdb=" N   ILE A 122 "
        model="   4" pdb=" CA  ILE A 122 "
        model="   4" pdb=" HA  ILE A 122 "
      ideal   model   delta    sigma   weight residual
     110.00  151.05  -41.05 3.00e+00 1.11e-01 1.87e+02
  angle model="   4" pdb=" N   MET A 128 "
        model="   4" pdb=" CA  MET A 128 "
        model="   4" pdb=" C   MET A 128 "
      ideal   model   delta    sigma   weight residual
     111.00   77.05   33.95 2.80e+00 1.28e-01 1.47e+02
  angle model="   4" pdb=" N   ILE A 131 "
        model="   4" pdb=" CA  ILE A 131 "
        model="   4" pdb=" CB  ILE A 131 "
      ideal   model   delta    sigma   weight residual
     111.50   91.50   20.00 1.70e+00 3.46e-01 1.38e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.14: 948
       26.14 -    52.29: 64
       52.29 -    78.43: 12
       78.43 -   104.58: 4
      104.58 -   130.72: 1
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="   4" pdb=" CA  MET A 128 "
           model="   4" pdb=" C   MET A 128 "
           model="   4" pdb=" N   ARG A 129 "
           model="   4" pdb=" CA  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   49.28  130.72     0      5.00e+00 4.00e-02 6.84e+02
  dihedral model="   4" pdb=" CA  VAL A 126 "
           model="   4" pdb=" C   VAL A 126 "
           model="   4" pdb=" N   ARG A 127 "
           model="   4" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   81.95   98.05     0      5.00e+00 4.00e-02 3.85e+02
  dihedral model="   4" pdb=" CA  LYS A 125 "
           model="   4" pdb=" C   LYS A 125 "
           model="   4" pdb=" N   VAL A 126 "
           model="   4" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   85.55   94.45     0      5.00e+00 4.00e-02 3.57e+02
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.068: 171
       1.068 -    2.135: 1
       2.135 -    3.203: 0
       3.203 -    4.270: 1
       4.270 -    5.338: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CB  ILE A 131 "
            model="   4" pdb=" CA  ILE A 131 "
            model="   4" pdb=" CG1 ILE A 131 "
            model="   4" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.69    5.34 2.00e-01 2.50e+01 7.12e+02
  chirality model="   4" pdb=" CA  TYR A  89 "
            model="   4" pdb=" N   TYR A  89 "
            model="   4" pdb=" C   TYR A  89 "
            model="   4" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.53    5.04 2.00e-01 2.50e+01 6.34e+02
  chirality model="   4" pdb=" CB  ILE A  77 "
            model="   4" pdb=" CA  ILE A  77 "
            model="   4" pdb=" CG1 ILE A  77 "
            model="   4" pdb=" CG2 ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.33    4.97 2.00e-01 2.50e+01 6.18e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  12 "   -0.088 2.00e-02 2.50e+03   4.11e-02 5.07e+01
        model="   4" pdb=" CG  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  12 "   -0.087 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  12 "    0.042 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  12 "    0.042 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  PHE A  67 "    0.055 2.00e-02 2.50e+03   3.91e-02 4.59e+01
        model="   4" pdb=" CG  PHE A  67 "   -0.021 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 PHE A  67 "   -0.032 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 PHE A  67 "    0.004 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 PHE A  67 "    0.015 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 PHE A  67 "   -0.021 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  PHE A  67 "    0.012 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 PHE A  67 "   -0.070 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 PHE A  67 "    0.037 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 PHE A  67 "    0.048 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 PHE A  67 "   -0.059 2.00e-02 2.50e+03
        model="   4" pdb=" HZ  PHE A  67 "    0.032 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  50 "    0.098 2.00e-02 2.50e+03   3.72e-02 4.16e+01
        model="   4" pdb=" CG  TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  50 "    0.049 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  50 "   -0.043 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 112
        2.13 -     2.74: 3843
        2.74 -     3.36: 6534
        3.36 -     3.98: 8016
        3.98 -     4.60: 11938
  Nonbonded interactions: 30443
  Sorted by model distance:
  nonbonded model="   4" pdb=" HA  TYR A  89 "
            model="   4" pdb=" H   LYS A 101 "
     model   vdw
     1.507 2.270
  nonbonded model="   4" pdb=" HA  LYS A 125 "
            model="   4" pdb=" H   ARG A 127 "
     model   vdw
     1.631 2.270
  nonbonded model="   4" pdb=" HA  ARG A 127 "
            model="   4" pdb=" H   ARG A 129 "
     model   vdw
     1.680 2.270
  nonbonded model="   4" pdb=" OD1 ASP A  44 "
            model="   4" pdb=" HG  SER A  46 "
     model   vdw
     1.778 1.850
  nonbonded model="   4" pdb=" H   SER A  90 "
            model="   4" pdb=" HA  GLN A 100 "
     model   vdw
     1.827 2.270
  ... (remaining 30438 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 463
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.459  0.032 2.10e-02 2.27e+03 2.38e+00
  bond model="   9" pdb=" CZ  ARG A 129 "
       model="   9" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.326  0.004 1.30e-02 5.92e+03 8.93e-02
  bond model="   9" pdb=" CZ  ARG A  58 "
       model="   9" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.326  0.004 1.30e-02 5.92e+03 7.78e-02
  bond model="   9" pdb=" CZ  ARG A 129 "
       model="   9" pdb=" NH1 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.323  1.327 -0.004 1.40e-02 5.10e+03 6.33e-02
  bond model="   9" pdb=" NE  ARG A 129 "
       model="   9" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 6.28e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.88 -   106.88: 66
      106.88 -   112.88: 2719
      112.88 -   118.88: 426
      118.88 -   124.88: 824
      124.88 -   130.88: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A 102 "
        model="   9" pdb=" CA  PRO A 102 "
        model="   9" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   9" pdb=" CB  PRO A 117 "
        model="   9" pdb=" CA  PRO A 117 "
        model="   9" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A  22 "
        model="   9" pdb=" CA  PRO A  22 "
        model="   9" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A 114 "
        model="   9" pdb=" CA  PRO A 114 "
        model="   9" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A  52 "
        model="   9" pdb=" CA  PRO A  52 "
        model="   9" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 875
       16.10 -    32.20: 62
       32.20 -    48.30: 55
       48.30 -    64.39: 36
       64.39 -    80.49: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CA  ASP A 110 "
           model="   9" pdb=" CB  ASP A 110 "
           model="   9" pdb=" CG  ASP A 110 "
           model="   9" pdb=" OD1 ASP A 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.87   57.87     1      2.00e+01 2.50e-03 1.12e+01
  dihedral model="   9" pdb=" N   TYR A  81 "
           model="   9" pdb=" CA  TYR A  81 "
           model="   9" pdb=" CB  TYR A  81 "
           model="   9" pdb=" CG  TYR A  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.30  -59.70     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   9" pdb=" CA  LYS A  63 "
           model="   9" pdb=" CB  LYS A  63 "
           model="   9" pdb=" CG  LYS A  63 "
           model="   9" pdb=" CD  LYS A  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.52   59.52     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 99
       0.019 -    0.038: 53
       0.038 -    0.057: 5
       0.057 -    0.076: 0
       0.076 -    0.095: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A  71 "
            model="   9" pdb=" N   ILE A  71 "
            model="   9" pdb=" C   ILE A  71 "
            model="   9" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.24e-01
  chirality model="   9" pdb=" CA  ILE A  51 "
            model="   9" pdb=" N   ILE A  51 "
            model="   9" pdb=" C   ILE A  51 "
            model="   9" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.22e-01
  chirality model="   9" pdb=" CA  ILE A  78 "
            model="   9" pdb=" N   ILE A  78 "
            model="   9" pdb=" C   ILE A  78 "
            model="   9" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.21e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  45 "    0.000 2.00e-02 2.50e+03   1.44e-03 6.18e-02
        model="   9" pdb=" CG  PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  45 "    0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  45 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A 111 "   -0.000 2.00e-02 2.50e+03   1.17e-03 4.07e-02
        model="   9" pdb=" CG  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  12 "    0.000 2.00e-02 2.50e+03   1.16e-03 4.06e-02
        model="   9" pdb=" CG  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  12 "    0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 83
        2.09 -     2.72: 3991
        2.72 -     3.34: 5986
        3.34 -     3.97: 7393
        3.97 -     4.60: 10870
  Nonbonded interactions: 28323
  Sorted by model distance:
  nonbonded model="   9" pdb="HD11 LEU A  93 "
            model="   9" pdb="HD13 LEU A  99 "
     model   vdw
     1.459 2.440
  nonbonded model="   9" pdb="HG12 VAL A  41 "
            model="   9" pdb="HG22 VAL A 112 "
     model   vdw
     1.581 2.440
  nonbonded model="   9" pdb="HG23 ILE A  37 "
            model="   9" pdb="HG21 ILE A 108 "
     model   vdw
     1.674 2.440
  nonbonded model="   9" pdb="HD13 LEU A   3 "
            model="   9" pdb="HD22 LEU A  53 "
     model   vdw
     1.727 2.440
  nonbonded model="   9" pdb=" O   GLU A  16 "
            model="   9" pdb=" HG1 THR A  20 "
     model   vdw
     1.750 1.850
  ... (remaining 28318 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 53
        1.23 -     1.42: 419
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" CD2 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.35e+00
  bond model="  11" pdb=" CZ  ARG A  21 "
       model="  11" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.63e+00
  bond model="  11" pdb=" CD2 HIS A 137 "
       model="  11" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.10e+00
  bond model="  11" pdb=" ND1 HIS A 135 "
       model="  11" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.84e+00
  bond model="  11" pdb=" CE1 HIS A 135 "
       model="  11" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.83e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.30 -   104.81: 53
      104.81 -   111.33: 2392
      111.33 -   117.84: 650
      117.84 -   124.36: 879
      124.36 -   130.87: 105
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" OE1 GLN A 100 "
        model="  11" pdb=" CD  GLN A 100 "
        model="  11" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  116.70    5.90 1.00e+00 1.00e+00 3.48e+01
  angle model="  11" pdb=" N   TYR A  89 "
        model="  11" pdb=" CA  TYR A  89 "
        model="  11" pdb=" CB  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.50  101.61    8.89 1.70e+00 3.46e-01 2.73e+01
  angle model="  11" pdb=" CA  HIS A 138 "
        model="  11" pdb=" CB  HIS A 138 "
        model="  11" pdb=" CG  HIS A 138 "
      ideal   model   delta    sigma   weight residual
     113.80  109.36    4.44 1.00e+00 1.00e+00 1.98e+01
  angle model="  11" pdb=" OE1 GLN A  28 "
        model="  11" pdb=" CD  GLN A  28 "
        model="  11" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.28    4.32 1.00e+00 1.00e+00 1.87e+01
  angle model="  11" pdb=" CB  HIS A 138 "
        model="  11" pdb=" CG  HIS A 138 "
        model="  11" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  125.61    5.59 1.30e+00 5.92e-01 1.85e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.03: 936
       18.03 -    36.06: 56
       36.06 -    54.08: 24
       54.08 -    72.11: 8
       72.11 -    90.14: 9
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  11" pdb=" CA  LEU A   2 "
           model="  11" pdb=" C   LEU A   2 "
           model="  11" pdb=" N   LEU A   3 "
           model="  11" pdb=" CA  LEU A   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.89   21.11     0      5.00e+00 4.00e-02 1.78e+01
  dihedral model="  11" pdb=" CA  LEU A 119 "
           model="  11" pdb=" C   LEU A 119 "
           model="  11" pdb=" N   GLU A 120 "
           model="  11" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.10   19.90     0      5.00e+00 4.00e-02 1.58e+01
  dihedral model="  11" pdb=" CA  ARG A 127 "
           model="  11" pdb=" C   ARG A 127 "
           model="  11" pdb=" N   MET A 128 "
           model="  11" pdb=" CA  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.73   19.27     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.051: 72
       0.051 -    0.102: 54
       0.102 -    0.153: 35
       0.153 -    0.204: 13
       0.204 -    0.255: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  LYS A 109 "
            model="  11" pdb=" N   LYS A 109 "
            model="  11" pdb=" C   LYS A 109 "
            model="  11" pdb=" CB  LYS A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality model="  11" pdb=" CA  ARG A 127 "
            model="  11" pdb=" N   ARG A 127 "
            model="  11" pdb=" C   ARG A 127 "
            model="  11" pdb=" CB  ARG A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality model="  11" pdb=" CA  ILE A 122 "
            model="  11" pdb=" N   ILE A 122 "
            model="  11" pdb=" C   ILE A 122 "
            model="  11" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  PHE A  67 "    0.300 2.00e-02 2.50e+03   1.21e-01 4.42e+02
        model="  11" pdb=" CG  PHE A  67 "   -0.032 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 PHE A  67 "   -0.064 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 PHE A  67 "   -0.080 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 PHE A  67 "   -0.023 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 PHE A  67 "   -0.008 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  PHE A  67 "    0.066 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 PHE A  67 "   -0.111 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 PHE A  67 "   -0.159 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 PHE A  67 "   -0.055 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 PHE A  67 "   -0.008 2.00e-02 2.50e+03
        model="  11" pdb=" HZ  PHE A  67 "    0.173 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  89 "    0.059 2.00e-02 2.50e+03   9.29e-02 2.59e+02
        model="  11" pdb=" CG  TYR A  89 "   -0.079 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  89 "   -0.005 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  89 "   -0.056 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  89 "    0.017 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  89 "    0.070 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  89 "   -0.160 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  89 "    0.030 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  89 "   -0.124 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  89 "    0.043 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  89 "    0.204 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  12 "   -0.154 2.00e-02 2.50e+03   6.86e-02 1.41e+02
        model="  11" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  12 "    0.033 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  12 "    0.027 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  12 "   -0.143 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  12 "    0.061 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  12 "    0.049 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  12 "    0.032 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  12 "    0.044 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 327
        2.29 -     2.87: 5038
        2.87 -     3.44: 5376
        3.44 -     4.02: 6811
        4.02 -     4.60: 10275
  Nonbonded interactions: 27827
  Sorted by model distance:
  nonbonded model="  11" pdb="HG23 ILE A 108 "
            model="  11" pdb=" HB2 TYR A 111 "
     model   vdw
     1.711 2.440
  nonbonded model="  11" pdb=" OD1 ASP A  44 "
            model="  11" pdb=" HG  SER A  46 "
     model   vdw
     1.768 1.850
  nonbonded model="  11" pdb=" OD1 ASP A  36 "
            model="  11" pdb=" HZ2 LYS A  40 "
     model   vdw
     1.780 1.850
  nonbonded model="  11" pdb=" OE2 GLU A  24 "
            model="  11" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.790 1.850
  nonbonded model="  11" pdb=" O   ILE A  30 "
            model="  11" pdb=" HG1 THR A  34 "
     model   vdw
     1.854 1.850
  ... (remaining 27822 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CB  ILE A  78 "
        model="   6" pdb=" CB  TYR A  89 "
        model="   6" pdb=" CB  TYR A  91 "
        model="   6" pdb=" CB  SER A  98 "
        model="   6" pdb=" CB  GLN A 100 "
        model="   6" pdb=" CB  GLU A 123 "
        model="   6" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.25 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.17
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CB  ILE A  78 "
        model="   3" pdb=" CB  LYS A  79 "
        model="   3" pdb=" CB  ILE A 122 "
        model="   3" pdb=" CB  GLU A 123 "
        model="   3" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.29 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 87
        1.23 -     1.43: 390
        1.43 -     1.62: 654
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   6" pdb=" N   GLY A  80 "
       model="   6" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.613 -0.162 1.60e-02 3.91e+03 1.03e+02
  bond model="   6" pdb=" C   TYR A  89 "
       model="   6" pdb=" N   SER A  90 "
    ideal  model  delta    sigma   weight residual
    1.329  1.421 -0.092 1.40e-02 5.10e+03 4.35e+01
  bond model="   6" pdb=" N   SER A  90 "
       model="   6" pdb=" CA  SER A  90 "
    ideal  model  delta    sigma   weight residual
    1.458  1.578 -0.120 1.90e-02 2.77e+03 4.02e+01
  bond model="   6" pdb=" CA  LYS A  79 "
       model="   6" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.652 -0.127 2.10e-02 2.27e+03 3.64e+01
  bond model="   6" pdb=" CA  LEU A  99 "
       model="   6" pdb=" C   LEU A  99 "
    ideal  model  delta    sigma   weight residual
    1.525  1.427  0.098 2.10e-02 2.27e+03 2.17e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       37.42 -    57.44: 1
       57.44 -    77.45: 1
       77.45 -    97.47: 18
       97.47 -   117.49: 3028
      117.49 -   137.50: 1031
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   6" pdb=" N   SER A  97 "
        model="   6" pdb=" CA  SER A  97 "
        model="   6" pdb=" HA  SER A  97 "
      ideal   model   delta    sigma   weight residual
     110.00   37.42   72.58 3.00e+00 1.11e-01 5.85e+02
  angle model="   6" pdb=" N   TYR A  81 "
        model="   6" pdb=" CA  TYR A  81 "
        model="   6" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     110.00   66.33   43.67 3.00e+00 1.11e-01 2.12e+02
  angle model="   6" pdb=" C   TYR A  89 "
        model="   6" pdb=" N   SER A  90 "
        model="   6" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70   97.90   23.80 1.80e+00 3.09e-01 1.75e+02
  angle model="   6" pdb=" CD2 LEU A  93 "
        model="   6" pdb=" CG  LEU A  93 "
        model="   6" pdb=" HG  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     108.00  135.40  -27.40 3.00e+00 1.11e-01 8.34e+01
  angle model="   6" pdb=" CB  LEU A  93 "
        model="   6" pdb=" CG  LEU A  93 "
        model="   6" pdb=" CD1 LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.70  137.50  -26.80 3.00e+00 1.11e-01 7.98e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.57: 944
       25.57 -    51.14: 54
       51.14 -    76.71: 13
       76.71 -   102.27: 3
      102.27 -   127.84: 3
  Dihedral angle restraints: 1017
    sinusoidal: 562
      harmonic: 455
  Sorted by residual:
  dihedral model="   6" pdb=" CA  LEU A  93 "
           model="   6" pdb=" C   LEU A  93 "
           model="   6" pdb=" N   GLY A  94 "
           model="   6" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -52.16 -127.84     0      5.00e+00 4.00e-02 6.54e+02
  dihedral model="   6" pdb=" CA  SER A  97 "
           model="   6" pdb=" C   SER A  97 "
           model="   6" pdb=" N   SER A  98 "
           model="   6" pdb=" CA  SER A  98 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   56.20  123.80     0      5.00e+00 4.00e-02 6.13e+02
  dihedral model="   6" pdb=" CA  THR A  92 "
           model="   6" pdb=" C   THR A  92 "
           model="   6" pdb=" N   LEU A  93 "
           model="   6" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   62.84  117.16     0      5.00e+00 4.00e-02 5.49e+02
  ... (remaining 1014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.105: 164
       1.105 -    2.210: 1
       2.210 -    3.315: 1
       3.315 -    4.420: 3
       4.420 -    5.524: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CA  TYR A  89 "
            model="   6" pdb=" N   TYR A  89 "
            model="   6" pdb=" C   TYR A  89 "
            model="   6" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.01    5.52 2.00e-01 2.50e+01 7.63e+02
  chirality model="   6" pdb=" CA  SER A  98 "
            model="   6" pdb=" N   SER A  98 "
            model="   6" pdb=" C   SER A  98 "
            model="   6" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.68    5.19 2.00e-01 2.50e+01 6.74e+02
  chirality model="   6" pdb=" CA  GLU A 123 "
            model="   6" pdb=" N   GLU A 123 "
            model="   6" pdb=" C   GLU A 123 "
            model="   6" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.51    5.02 2.00e-01 2.50e+01 6.31e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  81 "   -0.305 2.00e-02 2.50e+03   1.68e-01 8.50e+02
        model="   6" pdb=" CG  TYR A  81 "   -0.203 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  81 "    0.054 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  81 "    0.060 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  81 "    0.018 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  81 "    0.011 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  81 "   -0.115 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  81 "   -0.191 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  81 "    0.254 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  81 "    0.273 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  81 "    0.081 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  81 "    0.062 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  68 "    0.121 2.00e-02 2.50e+03   4.87e-02 7.10e+01
        model="   6" pdb=" CG  TYR A  68 "   -0.030 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  68 "   -0.023 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  68 "   -0.032 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  68 "   -0.017 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  68 "   -0.008 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  68 "    0.009 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  68 "    0.085 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  68 "   -0.022 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  68 "   -0.048 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  68 "   -0.030 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  68 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  12 "    0.098 2.00e-02 2.50e+03   4.48e-02 6.03e+01
        model="   6" pdb=" CG  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  12 "   -0.025 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  12 "    0.093 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  12 "   -0.046 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  12 "   -0.042 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.40 -     2.04: 75
        2.04 -     2.68: 3260
        2.68 -     3.32: 6894
        3.32 -     3.96: 8471
        3.96 -     4.60: 12677
  Nonbonded interactions: 31377
  Sorted by model distance:
  nonbonded model="   6" pdb=" H   THR A  92 "
            model="   6" pdb=" HA  LEU A  99 "
     model   vdw
     1.399 2.270
  nonbonded model="   6" pdb=" H   SER A  97 "
            model="   6" pdb=" HA  SER A  97 "
     model   vdw
     1.559 1.816
  nonbonded model="   6" pdb=" C   GLY A  96 "
            model="   6" pdb=" HA  SER A  97 "
     model   vdw
     1.632 2.336
  nonbonded model="   6" pdb=" H   TYR A  81 "
            model="   6" pdb=" HA  TYR A  81 "
     model   vdw
     1.643 1.816
  nonbonded model="   6" pdb=" N   SER A  90 "
            model="   6" pdb=" HA  GLN A 100 "
     model   vdw
     1.652 2.770
  ... (remaining 31372 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 58
        1.23 -     1.43: 417
        1.43 -     1.62: 656
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   3" pdb=" N   GLY A  80 "
       model="   3" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.564 -0.113 1.60e-02 3.91e+03 4.97e+01
  bond model="   3" pdb=" CA  LYS A  79 "
       model="   3" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.671 -0.146 2.10e-02 2.27e+03 4.86e+01
  bond model="   3" pdb=" CA  GLY A 121 "
       model="   3" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.616 -0.100 1.80e-02 3.09e+03 3.08e+01
  bond model="   3" pdb=" N   ARG A 127 "
       model="   3" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.561 -0.103 1.90e-02 2.77e+03 2.93e+01
  bond model="   3" pdb=" C   GLY A 121 "
       model="   3" pdb=" N   ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.329  1.399 -0.070 1.40e-02 5.10e+03 2.49e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       71.38 -    85.39: 3
       85.39 -    99.39: 14
       99.39 -   113.39: 2735
      113.39 -   127.39: 1286
      127.39 -   141.39: 41
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   3" pdb=" C   LYS A  79 "
        model="   3" pdb=" CA  LYS A  79 "
        model="   3" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.10  141.39  -31.29 1.90e+00 2.77e-01 2.71e+02
  angle model="   3" pdb=" C   ALA A 124 "
        model="   3" pdb=" CA  ALA A 124 "
        model="   3" pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     110.50  130.92  -20.42 1.50e+00 4.44e-01 1.85e+02
  angle model="   3" pdb=" C   ILE A  77 "
        model="   3" pdb=" CA  ILE A  77 "
        model="   3" pdb=" CB  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     111.60  138.37  -26.77 2.00e+00 2.50e-01 1.79e+02
  angle model="   3" pdb=" CB  TYR A  89 "
        model="   3" pdb=" CA  TYR A  89 "
        model="   3" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   71.38   37.62 3.00e+00 1.11e-01 1.57e+02
  angle model="   3" pdb=" C   LYS A  79 "
        model="   3" pdb=" CA  LYS A  79 "
        model="   3" pdb=" HA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     109.00   73.46   35.54 3.00e+00 1.11e-01 1.40e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.18: 946
       24.18 -    48.35: 60
       48.35 -    72.53: 8
       72.53 -    96.70: 5
       96.70 -   120.88: 2
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   3" pdb=" CA  TYR A  89 "
           model="   3" pdb=" C   TYR A  89 "
           model="   3" pdb=" N   SER A  90 "
           model="   3" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -59.12 -120.88     0      5.00e+00 4.00e-02 5.84e+02
  dihedral model="   3" pdb=" CA  ILE A  78 "
           model="   3" pdb=" C   ILE A  78 "
           model="   3" pdb=" N   LYS A  79 "
           model="   3" pdb=" CA  LYS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -65.68 -114.32     0      5.00e+00 4.00e-02 5.23e+02
  dihedral model="   3" pdb=" CA  VAL A 126 "
           model="   3" pdb=" C   VAL A 126 "
           model="   3" pdb=" N   ARG A 127 "
           model="   3" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   88.16   91.84     0      5.00e+00 4.00e-02 3.37e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.040: 167
       1.040 -    2.080: 1
       2.080 -    3.120: 0
       3.120 -    4.161: 2
       4.161 -    5.201: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   3" pdb=" CB  ILE A 131 "
            model="   3" pdb=" CA  ILE A 131 "
            model="   3" pdb=" CG1 ILE A 131 "
            model="   3" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.56    5.20 2.00e-01 2.50e+01 6.76e+02
  chirality model="   3" pdb=" CB  ILE A  78 "
            model="   3" pdb=" CA  ILE A  78 "
            model="   3" pdb=" CG1 ILE A  78 "
            model="   3" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.38    5.02 2.00e-01 2.50e+01 6.31e+02
  chirality model="   3" pdb=" CA  ILE A 122 "
            model="   3" pdb=" N   ILE A 122 "
            model="   3" pdb=" C   ILE A 122 "
            model="   3" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -2.53    4.96 2.00e-01 2.50e+01 6.16e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  91 "    0.523 2.00e-02 2.50e+03   2.31e-01 1.60e+03
        model="   3" pdb=" CG  TYR A  91 "    0.015 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  91 "   -0.089 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  91 "   -0.124 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  91 "   -0.087 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  91 "   -0.052 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  91 "    0.069 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  91 "    0.439 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  91 "   -0.158 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  91 "   -0.264 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  91 "   -0.188 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  91 "   -0.084 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A 105 "   -0.203 2.00e-02 2.50e+03   8.56e-02 2.20e+02
        model="   3" pdb=" CG  TYR A 105 "    0.018 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A 105 "    0.039 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A 105 "    0.048 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A 105 "    0.026 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A 105 "    0.015 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A 105 "   -0.050 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A 105 "   -0.146 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A 105 "    0.061 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A 105 "    0.091 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A 105 "    0.067 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A 105 "    0.035 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A 111 "    0.139 2.00e-02 2.50e+03   5.41e-02 8.78e+01
        model="   3" pdb=" CG  TYR A 111 "   -0.035 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A 111 "   -0.034 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A 111 "   -0.030 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A 111 "    0.087 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A 111 "   -0.049 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A 111 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 95
        2.09 -     2.72: 3601
        2.72 -     3.34: 6661
        3.34 -     3.97: 8136
        3.97 -     4.60: 12133
  Nonbonded interactions: 30626
  Sorted by model distance:
  nonbonded model="   3" pdb=" HB1 ALA A 124 "
            model="   3" pdb=" H   VAL A 126 "
     model   vdw
     1.461 2.270
  nonbonded model="   3" pdb=" HB  ILE A  77 "
            model="   3" pdb=" HB3 LYS A  79 "
     model   vdw
     1.475 2.440
  nonbonded model="   3" pdb=" HB3 MET A 128 "
            model="   3" pdb=" H   SER A 130 "
     model   vdw
     1.556 2.270
  nonbonded model="   3" pdb=" HA  SER A  90 "
            model="   3" pdb=" HB3 LEU A  99 "
     model   vdw
     1.695 2.440
  nonbonded model="   3" pdb=" HA  GLU A 123 "
            model="   3" pdb=" HB3 ALA A 124 "
     model   vdw
     1.723 2.440
  ... (remaining 30621 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CB  LYS A  79 "
        model="   4" pdb=" CB  TYR A  89 "
        model="   4" pdb=" CB  SER A  90 "
        model="   4" pdb=" CB  LEU A 119 "
        model="   4" pdb=" CB  GLU A 123 "
        model="   4" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 58
        1.23 -     1.43: 417
        1.43 -     1.62: 648
        1.62 -     1.82: 13
  Bond restraints: 2242
  Sorted by residual:
  bond model="   4" pdb=" N   MET A 128 "
       model="   4" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.677 -0.219 1.90e-02 2.77e+03 1.33e+02
  bond model="   4" pdb=" N   LEU A 132 "
       model="   4" pdb=" CA  LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.458  1.670 -0.212 1.90e-02 2.77e+03 1.25e+02
  bond model="   4" pdb=" N   VAL A 126 "
       model="   4" pdb=" CA  VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.666 -0.208 1.90e-02 2.77e+03 1.20e+02
  bond model="   4" pdb=" CA  GLY A 121 "
       model="   4" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.699 -0.183 1.80e-02 3.09e+03 1.04e+02
  bond model="   4" pdb=" N   ILE A 122 "
       model="   4" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.646 -0.188 1.90e-02 2.77e+03 9.80e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       84.48 -    96.25: 14
       96.25 -   108.03: 615
      108.03 -   119.81: 2635
      119.81 -   131.58: 803
      131.58 -   143.36: 12
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   4" pdb=" C   LEU A 132 "
        model="   4" pdb=" N   GLU A 133 "
        model="   4" pdb=" CA  GLU A 133 "
      ideal   model   delta    sigma   weight residual
     121.70  143.36  -21.66 1.80e+00 3.09e-01 1.45e+02
  angle model="   4" pdb=" C   LYS A  79 "
        model="   4" pdb=" CA  LYS A  79 "
        model="   4" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.10   88.76   21.34 1.90e+00 2.77e-01 1.26e+02
  angle model="   4" pdb=" CA  VAL A 126 "
        model="   4" pdb=" C   VAL A 126 "
        model="   4" pdb=" N   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     116.20   96.22   19.98 2.00e+00 2.50e-01 9.98e+01
  angle model="   4" pdb=" C   GLU A 123 "
        model="   4" pdb=" CA  GLU A 123 "
        model="   4" pdb=" CB  GLU A 123 "
      ideal   model   delta    sigma   weight residual
     110.10  128.50  -18.40 1.90e+00 2.77e-01 9.37e+01
  angle model="   4" pdb=" C   LEU A  39 "
        model="   4" pdb=" CA  LEU A  39 "
        model="   4" pdb=" CB  LEU A  39 "
      ideal   model   delta    sigma   weight residual
     110.10  128.27  -18.17 1.90e+00 2.77e-01 9.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.52: 931
       23.52 -    47.05: 63
       47.05 -    70.57: 16
       70.57 -    94.09: 3
       94.09 -   117.61: 4
  Dihedral angle restraints: 1017
    sinusoidal: 562
      harmonic: 455
  Sorted by residual:
  dihedral model="   4" pdb=" CA  LYS A 125 "
           model="   4" pdb=" C   LYS A 125 "
           model="   4" pdb=" N   VAL A 126 "
           model="   4" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   62.39  117.61     0      5.00e+00 4.00e-02 5.53e+02
  dihedral model="   4" pdb=" CA  VAL A 126 "
           model="   4" pdb=" C   VAL A 126 "
           model="   4" pdb=" N   ARG A 127 "
           model="   4" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   75.20  104.80     0      5.00e+00 4.00e-02 4.39e+02
  dihedral model="   4" pdb=" CA  ILE A  78 "
           model="   4" pdb=" C   ILE A  78 "
           model="   4" pdb=" N   LYS A  79 "
           model="   4" pdb=" CA  LYS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -77.47 -102.53     0      5.00e+00 4.00e-02 4.21e+02
  ... (remaining 1014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.132: 166
       1.132 -    2.265: 0
       2.265 -    3.397: 0
       3.397 -    4.529: 3
       4.529 -    5.661: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CA  MET A 128 "
            model="   4" pdb=" N   MET A 128 "
            model="   4" pdb=" C   MET A 128 "
            model="   4" pdb=" CB  MET A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.15    5.66 2.00e-01 2.50e+01 8.01e+02
  chirality model="   4" pdb=" CA  LYS A  79 "
            model="   4" pdb=" N   LYS A  79 "
            model="   4" pdb=" C   LYS A  79 "
            model="   4" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.13    5.64 2.00e-01 2.50e+01 7.96e+02
  chirality model="   4" pdb=" CB  ILE A  78 "
            model="   4" pdb=" CA  ILE A  78 "
            model="   4" pdb=" CG1 ILE A  78 "
            model="   4" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.61    5.25 2.00e-01 2.50e+01 6.89e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  50 "   -0.181 2.00e-02 2.50e+03   7.23e-02 1.57e+02
        model="   4" pdb=" CG  TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  50 "    0.042 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  50 "    0.039 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  50 "   -0.122 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  50 "    0.069 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  50 "    0.060 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  50 "    0.033 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  91 "   -0.118 2.00e-02 2.50e+03   7.21e-02 1.56e+02
        model="   4" pdb=" CG  TYR A  91 "    0.035 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  91 "    0.063 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  91 "    0.022 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  91 "   -0.039 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  91 "   -0.022 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  91 "   -0.006 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  91 "   -0.034 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  91 "    0.148 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  91 "    0.065 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  91 "   -0.117 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CA  LYS A 125 "   -0.030 2.00e-02 2.50e+03   6.41e-02 4.11e+01
        model="   4" pdb=" C   LYS A 125 "    0.111 2.00e-02 2.50e+03
        model="   4" pdb=" O   LYS A 125 "   -0.046 2.00e-02 2.50e+03
        model="   4" pdb=" N   VAL A 126 "   -0.034 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 143
        2.14 -     2.76: 4033
        2.76 -     3.37: 6526
        3.37 -     3.99: 8252
        3.99 -     4.60: 12309
  Nonbonded interactions: 31263
  Sorted by model distance:
  nonbonded model="   4" pdb=" HA  ILE A  77 "
            model="   4" pdb=" HA  LYS A  79 "
     model   vdw
     1.527 2.440
  nonbonded model="   4" pdb=" HA  LYS A 125 "
            model="   4" pdb=" H   ARG A 127 "
     model   vdw
     1.552 2.270
  nonbonded model="   4" pdb=" HB2 ASP A 103 "
            model="   4" pdb=" H   GLU A 133 "
     model   vdw
     1.575 2.270
  nonbonded model="   4" pdb=" HB3 GLU A 123 "
            model="   4" pdb=" H   LYS A 125 "
     model   vdw
     1.614 2.270
  nonbonded model="   4" pdb=" OD2 ASP A  36 "
            model="   4" pdb=" HH  TYR A  68 "
     model   vdw
     1.775 1.850
  ... (remaining 31258 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CB  LYS A  79 "
        model="   4" pdb=" CB  ILE A 122 "
        model="   4" pdb=" CB  GLU A 123 "
        model="   4" pdb=" CB  VAL A 126 "
        model="   4" pdb=" CB  MET A 128 "
        model="   4" pdb=" CB  SER A 130 "
        model="   4" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  246

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 55
        1.23 -     1.43: 422
        1.43 -     1.62: 653
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   4" pdb=" CA  ALA A 124 "
       model="   4" pdb=" C   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.525  1.743 -0.218 2.10e-02 2.27e+03 1.07e+02
  bond model="   4" pdb=" N   LYS A 125 "
       model="   4" pdb=" CA  LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.620 -0.162 1.90e-02 2.77e+03 7.29e+01
  bond model="   4" pdb=" C   ALA A 124 "
       model="   4" pdb=" N   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.329  1.440 -0.111 1.40e-02 5.10e+03 6.29e+01
  bond model="   4" pdb=" N   GLY A  80 "
       model="   4" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.572 -0.121 1.60e-02 3.91e+03 5.73e+01
  bond model="   4" pdb=" N   SER A 130 "
       model="   4" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.601 -0.143 1.90e-02 2.77e+03 5.69e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       63.36 -    85.23: 4
       85.23 -   107.10: 487
      107.10 -   128.97: 3568
      128.97 -   150.84: 19
      150.84 -   172.72: 1
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   4" pdb=" N   TYR A  89 "
        model="   4" pdb=" CA  TYR A  89 "
        model="   4" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.00  172.72  -62.72 3.00e+00 1.11e-01 4.37e+02
  angle model="   4" pdb=" C   VAL A 126 "
        model="   4" pdb=" N   ARG A 127 "
        model="   4" pdb=" CA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     121.70   86.94   34.76 1.80e+00 3.09e-01 3.73e+02
  angle model="   4" pdb=" C   TYR A  89 "
        model="   4" pdb=" CA  TYR A  89 "
        model="   4" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   63.36   45.64 3.00e+00 1.11e-01 2.31e+02
  angle model="   4" pdb=" N   VAL A 126 "
        model="   4" pdb=" CA  VAL A 126 "
        model="   4" pdb=" C   VAL A 126 "
      ideal   model   delta    sigma   weight residual
     111.00   69.99   41.01 2.80e+00 1.28e-01 2.15e+02
  angle model="   4" pdb=" CB  TYR A  89 "
        model="   4" pdb=" CA  TYR A  89 "
        model="   4" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   70.16   38.84 3.00e+00 1.11e-01 1.68e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.08: 945
       24.08 -    48.15: 48
       48.15 -    72.23: 14
       72.23 -    96.30: 4
       96.30 -   120.38: 4
  Dihedral angle restraints: 1015
    sinusoidal: 562
      harmonic: 453
  Sorted by residual:
  dihedral model="   4" pdb=" CA  ILE A  77 "
           model="   4" pdb=" C   ILE A  77 "
           model="   4" pdb=" N   ILE A  78 "
           model="   4" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   59.62  120.38     0      5.00e+00 4.00e-02 5.80e+02
  dihedral model="   4" pdb=" C   TYR A  89 "
           model="   4" pdb=" N   TYR A  89 "
           model="   4" pdb=" CA  TYR A  89 "
           model="   4" pdb=" CB  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -178.50   55.90     0      2.50e+00 1.60e-01 5.00e+02
  dihedral model="   4" pdb=" N   TYR A  89 "
           model="   4" pdb=" C   TYR A  89 "
           model="   4" pdb=" CA  TYR A  89 "
           model="   4" pdb=" CB  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  178.10  -55.30     0      2.50e+00 1.60e-01 4.89e+02
  ... (remaining 1012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.150: 165
       1.150 -    2.299: 0
       2.299 -    3.449: 3
       3.449 -    4.599: 3
       4.599 -    5.748: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CA  LYS A  79 "
            model="   4" pdb=" N   LYS A  79 "
            model="   4" pdb=" C   LYS A  79 "
            model="   4" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.24    5.75 2.00e-01 2.50e+01 8.26e+02
  chirality model="   4" pdb=" CB  ILE A  78 "
            model="   4" pdb=" CA  ILE A  78 "
            model="   4" pdb=" CG1 ILE A  78 "
            model="   4" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.67    5.32 2.00e-01 2.50e+01 7.07e+02
  chirality model="   4" pdb=" CA  GLU A 123 "
            model="   4" pdb=" N   GLU A 123 "
            model="   4" pdb=" C   GLU A 123 "
            model="   4" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.57    5.08 2.00e-01 2.50e+01 6.46e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  91 "   -0.227 2.00e-02 2.50e+03   8.80e-02 2.32e+02
        model="   4" pdb=" CG  TYR A  91 "    0.036 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  91 "    0.063 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  91 "    0.044 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  91 "    0.021 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  91 "   -0.020 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  91 "   -0.117 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  91 "    0.119 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  91 "    0.064 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  91 "   -0.019 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  91 "    0.033 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  89 "    0.129 2.00e-02 2.50e+03   5.69e-02 9.71e+01
        model="   4" pdb=" CG  TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  89 "   -0.018 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  89 "   -0.038 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  89 "   -0.027 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  89 "   -0.008 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  89 "    0.107 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  89 "   -0.073 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  89 "   -0.050 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  89 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  PHE A  15 "   -0.136 2.00e-02 2.50e+03   5.34e-02 8.56e+01
        model="   4" pdb=" CG  PHE A  15 "    0.035 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 PHE A  15 "    0.043 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 PHE A  15 "    0.027 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 PHE A  15 "   -0.007 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 PHE A  15 "    0.009 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  PHE A  15 "   -0.022 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 PHE A  15 "    0.081 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 PHE A  15 "    0.035 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 PHE A  15 "   -0.030 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 PHE A  15 "    0.016 2.00e-02 2.50e+03
        model="   4" pdb=" HZ  PHE A  15 "   -0.051 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 148
        2.15 -     2.76: 4035
        2.76 -     3.37: 6574
        3.37 -     3.99: 7946
        3.99 -     4.60: 11803
  Nonbonded interactions: 30506
  Sorted by model distance:
  nonbonded model="   4" pdb=" HA  TYR A  89 "
            model="   4" pdb=" HB2 TYR A  89 "
     model   vdw
     1.533 1.952
  nonbonded model="   4" pdb=" HA  LYS A  79 "
            model="   4" pdb=" HA  LEU A  93 "
     model   vdw
     1.611 2.440
  nonbonded model="   4" pdb=" HA  TYR A  91 "
            model="   4" pdb=" HA  LEU A  99 "
     model   vdw
     1.699 2.440
  nonbonded model="   4" pdb=" H   THR A  92 "
            model="   4" pdb=" HB2 LEU A  99 "
     model   vdw
     1.712 2.270
  nonbonded model="   4" pdb=" HB  ILE A  78 "
            model="   4" pdb=" HA2 GLY A  94 "
     model   vdw
     1.748 2.440
  ... (remaining 30501 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.065 (Z=  3.403)
  Mean delta:    0.013 (Z=  0.688)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        121.70   132.52   -10.82  1.80e+00  3.61e+01   6.0*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   116.63     5.97  1.00e+00  3.56e+01   6.0*sigma
   A 135  HIS  CA
   A 135  HIS  CB
   A 135  HIS  CG        113.80   108.05     5.75  1.00e+00  3.31e+01   5.8*sigma
   A 134  HIS  CA
   A 134  HIS  CB
   A 134  HIS  CG        113.80   108.35     5.45  1.00e+00  2.97e+01   5.5*sigma
   A 136  HIS  C
   A 136  HIS  CA
   A 136  HIS  CB        110.10   119.18    -9.08  1.90e+00  2.28e+01   4.8*sigma
   A 133  GLU  CA
   A 133  GLU  CB
   A 133  GLU  CG        114.10   122.97    -8.87  2.00e+00  1.97e+01   4.4*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.52     5.68  1.30e+00  1.91e+01   4.4*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N         116.20   107.57     8.63  2.00e+00  1.86e+01   4.3*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.85     5.35  1.30e+00  1.69e+01   4.1*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   129.07    -7.37  1.80e+00  1.68e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.60     4.00  1.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   10.820 (Z=  6.011)
  Mean delta:    2.088 (Z=  1.155)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   132.76    47.24  5.00e+00  8.93e+01   9.4*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00  -147.86   -32.14  5.00e+00  4.13e+01   6.4*sigma
   A 100  GLN  CA
   A 100  GLN  C
   A 101  LYS  N
   A 101  LYS  CA        180.00  -156.64   -23.36  5.00e+00  2.18e+01   4.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   159.71    20.29  5.00e+00  1.65e+01   4.1*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00  -159.81   -20.19  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.038
  Max. delta:   86.602
  Mean delta:   16.320

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 136  HIS  CA
   A 136  HIS  N
   A 136  HIS  C
   A 136  HIS  CB          2.51    -2.12     4.63  2.00e-01  5.35e+02  23.1*sigma
   A  83  THR  CA
   A  83  THR  N
   A  83  THR  C
   A  83  THR  CB          2.53    -1.97     4.50  2.00e-01  5.06e+02  22.5*sigma
   A 134  HIS  CA
   A 134  HIS  N
   A 134  HIS  C
   A 134  HIS  CB          2.51    -1.77     4.28  2.00e-01  4.57e+02  21.4*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     1.37     1.14  2.00e-01  3.25e+01   5.7*sigma

  Min. delta:    0.001
  Max. delta:    4.625
  Mean delta:    0.600

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  ND1
   A 134  HIS  CD2
   A 134  HIS  CE1
   A 134  HIS  NE2           0.050       0.094       37.12   4.7*sigma

  Min. delta:    0.000
  Max. delta:    0.072
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  83  THR  HA , Angle C-CA-HA, observed: 96.254, delta from target: 12.746
   A  81  TYR  HA , Angle C-CA-HA, observed: 92.378, delta from target: 16.622

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.065   2242  Z= 0.490
    Angle     :  1.895  16.622   4079  Z= 0.848
    Chirality :  0.600   4.625    176
    Planarity :  0.012   0.064    327
    Dihedral  : 13.886  86.602    769
    Min Nonbonded Distance : 1.529
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.11 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  8.06 %
      Favored  : 87.90 %
    Cbeta Deviations :  3.03 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 1.53 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.56 (0.70), residues: 137
    helix: -0.50 (0.56), residues: 70
    sheet:  None (None), residues: 0
    loop : -1.60 (0.83), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.007   HIS A 134 
   PHE   0.046   0.012   PHE A  15 
   TYR   0.157   0.026   TYR A  89 
   ARG   0.035   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.007   HIS A 134 
   PHE   0.031   0.012   PHE A  15 
   TYR   0.136   0.030   TYR A  89 
   ARG   0.006   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 134  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.038 (Z=  2.581)
  Mean delta:    0.013 (Z=  0.659)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   132.95   -11.25  1.80e+00  3.91e+01   6.3*sigma
   A  72  ASN  OD1
   A  72  ASN  CG
   A  72  ASN  ND2       122.60   117.67     4.93  1.00e+00  2.43e+01   4.9*sigma
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        121.70   130.02    -8.32  1.80e+00  2.14e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.00     4.60  1.00e+00  2.12e+01   4.6*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.27     4.33  1.00e+00  1.88e+01   4.3*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.66     5.54  1.30e+00  1.81e+01   4.3*sigma
   A 133  GLU  N
   A 133  GLU  CA
   A 133  GLU  C         111.00   122.33   -11.33  2.80e+00  1.64e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   11.363 (Z=  6.251)
  Mean delta:    1.912 (Z=  1.050)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00   117.52    62.48  5.00e+00  1.56e+02  12.5*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00  -140.06   -39.94  5.00e+00  6.38e+01   8.0*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -142.43   -37.57  5.00e+00  5.65e+01   7.5*sigma

  Min. delta:    0.024
  Max. delta:   62.485
  Mean delta:   13.836

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 133  GLU  CA
   A 133  GLU  N
   A 133  GLU  C
   A 133  GLU  CB          2.51    -1.52     4.03  2.00e-01  4.06e+02  20.1*sigma

  Min. delta:    0.000
  Max. delta:    4.029
  Mean delta:    0.316

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.098       0.190      190.77   9.5*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.047       0.092       43.52   4.6*sigma
   A 103  ASP  CB
   A 103  ASP  CG
   A 103  ASP  OD1
   A 103  ASP  OD2           0.050       0.086       24.70   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.098
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 133  GLU  HA , Angle N-CA-HA, observed: 93.751, delta from target: 16.249

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.740  16.249   4079  Z= 0.774
    Chirality :  0.316   4.029    176
    Planarity :  0.012   0.093    327
    Dihedral  : 11.924  83.778    769
    Min Nonbonded Distance : 1.671
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  5.84 %
      Favored  : 90.51 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.03 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.30 (0.66), residues: 137
    helix: -0.05 (0.59), residues: 57
    sheet:  None (None), residues: 0
    loop : -1.51 (0.69), residues: 80
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.005   HIS A 137 
   PHE   0.080   0.026   PHE A  67 
   TYR   0.240   0.022   TYR A 111 
   ARG   0.057   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.005   HIS A 137 
   PHE   0.040   0.021   PHE A  67 
   TYR   0.190   0.024   TYR A 111 
   ARG   0.007   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  92.70 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     4
  Clashscore            =   3.61
  RMS(bonds)            =   0.0095
  RMS(angles)           =   1.89
  MolProbity score      =   2.07

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 128  MET  N
   A 128  MET  CA          1.46     1.73    -0.27  1.90e-02  1.98e+02  14.1*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.64    -0.18  1.90e-02  8.76e+01   9.4*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.62    -0.16  1.90e-02  7.31e+01   8.6*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.60    -0.14  1.90e-02  5.51e+01   7.4*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.64    -0.13  1.80e-02  5.01e+01   7.1*sigma
   A 128  MET  CA
   A 128  MET  C           1.52     1.40     0.12  2.10e-02  3.47e+01   5.9*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.41    -0.08  1.40e-02  3.46e+01   5.9*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.63    -0.10  2.10e-02  2.36e+01   4.9*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.55    -0.09  1.90e-02  2.26e+01   4.8*sigma
   A 132  LEU  N
   A 132  LEU  CA          1.46     1.55    -0.09  1.90e-02  2.24e+01   4.7*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.26     0.07  1.40e-02  2.22e+01   4.7*sigma
   A 119  LEU  N
   A 119  LEU  CA          1.46     1.54    -0.08  1.90e-02  1.82e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.267 (Z= 14.070)
  Mean delta:    0.021 (Z=  1.085)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   144.41   -22.71  1.80e+00  1.59e+02  12.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20    93.78    22.42  2.00e+00  1.26e+02  11.2*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   141.71   -20.01  1.80e+00  1.24e+02  11.1*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    93.87    17.63  1.70e+00  1.07e+02  10.4*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   103.49    18.21  1.80e+00  1.02e+02  10.1*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    82.83    28.17  2.80e+00  1.01e+02  10.1*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   135.72   -19.52  2.00e+00  9.53e+01   9.8*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   139.14   -17.44  1.80e+00  9.39e+01   9.7*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   127.39   -17.29  1.90e+00  8.28e+01   9.1*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   125.50   -15.00  1.70e+00  7.79e+01   8.8*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   128.91   -17.31  2.00e+00  7.49e+01   8.7*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   123.17   -12.67  1.50e+00  7.13e+01   8.4*sigma
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        121.70   136.65   -14.95  1.80e+00  6.89e+01   8.3*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   111.69    11.31  1.60e+00  5.00e+01   7.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.38   -10.48  1.50e+00  4.88e+01   7.0*sigma
   A 137  HIS  CA
   A 137  HIS  CB
   A 137  HIS  CG        113.80   120.51    -6.71  1.00e+00  4.50e+01   6.7*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   121.85   -11.35  1.70e+00  4.46e+01   6.7*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   133.69   -11.99  1.80e+00  4.44e+01   6.7*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.80    -6.20  1.00e+00  3.85e+01   6.2*sigma
   A 137  HIS  C
   A 137  HIS  CA
   A 137  HIS  CB        110.10   121.24   -11.14  1.90e+00  3.44e+01   5.9*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   120.39    -9.89  1.70e+00  3.38e+01   5.8*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.69    -9.99  1.80e+00  3.08e+01   5.5*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.66   -11.06  2.00e+00  3.06e+01   5.5*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.60    -9.90  1.80e+00  3.02e+01   5.5*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50   102.28     9.22  1.70e+00  2.94e+01   5.4*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   119.59    -9.09  1.70e+00  2.86e+01   5.3*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   124.38     6.82  1.30e+00  2.75e+01   5.2*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N         116.20   126.46   -10.26  2.00e+00  2.63e+01   5.1*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   119.18    -9.08  1.90e+00  2.28e+01   4.8*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   130.22    -8.52  1.80e+00  2.24e+01   4.7*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50   119.40    -7.90  1.70e+00  2.16e+01   4.6*sigma
   A 138  HIS  O
   A 138  HIS  C
   A 139  HIS  N         123.00   115.75     7.25  1.60e+00  2.05e+01   4.5*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   107.52     8.68  2.00e+00  1.88e+01   4.3*sigma
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        121.70   129.39    -7.69  1.80e+00  1.82e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.35     4.25  1.00e+00  1.80e+01   4.2*sigma
   A 129  ARG  C
   A 129  ARG  CA
   A 129  ARG  CB        110.10   118.14    -8.04  1.90e+00  1.79e+01   4.2*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   129.25    -7.55  1.80e+00  1.76e+01   4.2*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   117.96    -4.16  1.00e+00  1.73e+01   4.2*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  ND1       122.70   128.88    -6.18  1.50e+00  1.70e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   127.67    -6.87  1.70e+00  1.64e+01   4.0*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.58     4.02  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   28.171 (Z= 12.618)
  Mean delta:    3.062 (Z=  1.654)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    54.82   125.18  5.00e+00  6.27e+02  25.0*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    64.71   115.29  5.00e+00  5.32e+02  23.1*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    71.07   108.93  5.00e+00  4.75e+02  21.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    73.88   106.12  5.00e+00  4.50e+02  21.2*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00    78.12   101.88  5.00e+00  4.15e+02  20.4*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   -85.16   -94.84  5.00e+00  3.60e+02  19.0*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -108.24   -71.76  5.00e+00  2.06e+02  14.4*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   110.23    69.77  5.00e+00  1.95e+02  14.0*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -115.21   -64.79  5.00e+00  1.68e+02  13.0*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   115.44    64.56  5.00e+00  1.67e+02  12.9*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   125.13    54.87  5.00e+00  1.20e+02  11.0*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   129.46    50.54  5.00e+00  1.02e+02  10.1*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   133.64    46.36  5.00e+00  8.60e+01   9.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA          0.00    43.79   -43.79  5.00e+00  7.67e+01   8.8*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -141.55   -38.45  5.00e+00  5.91e+01   7.7*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   149.54    30.46  5.00e+00  3.71e+01   6.1*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   150.88    29.12  5.00e+00  3.39e+01   5.8*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -152.60   -27.40  5.00e+00  3.00e+01   5.5*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   154.39    25.61  5.00e+00  2.62e+01   5.1*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   157.92    22.08  5.00e+00  1.95e+01   4.4*sigma

  Min. delta:    0.002
  Max. delta:  125.184
  Mean delta:   21.475

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.65     5.16  2.00e-01  6.65e+02  25.8*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.52     5.07  2.00e-01  6.43e+02  25.4*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.55     5.06  2.00e-01  6.41e+02  25.3*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.34     4.99  2.00e-01  6.22e+02  24.9*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.28     4.71  2.00e-01  5.55e+02  23.6*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.91     4.34  2.00e-01  4.71e+02  21.7*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -1.78     4.29  2.00e-01  4.60e+02  21.4*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.88     3.31  2.00e-01  2.74e+02  16.6*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.34     1.17  2.00e-01  3.44e+01   5.9*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53     1.36     1.17  2.00e-01  3.42e+01   5.9*sigma

  Min. delta:    0.000
  Max. delta:    5.159
  Mean delta:    1.013

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O
   A 127  ARG  N             0.131       0.097      171.41   4.8*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.050       0.087       49.10   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.131
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 126  VAL  H  , Angle C-N-H, observed: 112.087, delta from target: 12.213
   A  78  ILE  HB , Angle CA-CB-HB, observed: 96.579, delta from target: 12.421
   A  92  THR  HA , Angle CB-CA-HA, observed: 95.455, delta from target: 13.545
   A  78  ILE  HA , Angle C-CA-HA, observed: 93.466, delta from target: 15.534
   A 131  ILE  HA , Angle N-CA-HA, observed: 127.009, delta from target: -17.009
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.312, delta from target: 17.688
   A 128  MET  HA , Angle N-CA-HA, observed: 128.586, delta from target: -18.586
   A 122  ILE  HA , Angle C-CA-HA, observed: 90.264, delta from target: 18.736
   A 131  ILE  HA , Angle C-CA-HA, observed: 89.776, delta from target: 19.224
   A  51  ILE  HA , Angle CB-CA-HA, observed: 89.197, delta from target: 19.803
   A 127  ARG  HA , Angle CB-CA-HA, observed: 66.005, delta from target: 42.995

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.015   0.267   2242  Z= 0.772
    Angle     :  2.696  42.995   4079  Z= 1.203
    Chirality :  1.013   5.159    176
    Planarity :  0.013   0.131    327
    Dihedral  : 17.070 125.184    769
    Min Nonbonded Distance : 1.387
  
  Molprobity Statistics.
    All-atom Clashscore : 14.88
    Ramachandran Plot:
      Outliers :  7.30 %
      Allowed  : 10.22 %
      Favored  : 82.48 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  4.84 %
      Favored  : 88.71 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 1.53 %
      Twisted Proline : 14.29 %
      Twisted General : 11.45 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.07 (0.71), residues: 137
    helix: -1.82 (0.54), residues: 70
    sheet:  None (None), residues: 0
    loop : -0.67 (0.86), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.054   0.011   PHE A  67 
   TYR   0.119   0.015   TYR A  50 
   ARG   0.027   0.005   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.026   0.009   PHE A  67 
   TYR   0.096   0.017   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================

  Ramachandran outliers =   3.65 %
                favored =  90.51 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     1
  Clashscore            =   2.71
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.74
  MolProbity score      =   1.75

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   7.30 %
                favored =  82.48 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    14
  Clashscore            =  14.88
  RMS(bonds)            =   0.0148
  RMS(angles)           =   2.70
  MolProbity score      =   2.99

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.570)
  Mean delta:    0.013 (Z=  0.659)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   130.55    -8.85  1.80e+00  2.42e+01   4.9*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   117.79     4.81  1.00e+00  2.31e+01   4.8*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.03     4.57  1.00e+00  2.09e+01   4.6*sigma
   A  56  THR  OG1
   A  56  THR  CB
   A  56  THR  CG2       109.30   100.78     8.52  2.00e+00  1.81e+01   4.3*sigma
   A  56  THR  CA
   A  56  THR  CB
   A  56  THR  OG1       109.60   115.94    -6.34  1.50e+00  1.79e+01   4.2*sigma

  Min. delta:    0.004 (Z=  0.001)
  Max. delta:    8.854 (Z=  4.919)
  Mean delta:    1.871 (Z=  1.019)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -153.54   -26.46  5.00e+00  2.80e+01   5.3*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   154.70    25.30  5.00e+00  2.56e+01   5.1*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -158.02   -21.98  5.00e+00  1.93e+01   4.4*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   159.15    20.85  5.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.040
  Max. delta:   85.665
  Mean delta:   18.081

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51    -2.14     4.65  2.00e-01  5.40e+02  23.2*sigma

  Min. delta:    0.000
  Max. delta:    4.650
  Mean delta:    0.361

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.101       0.185      204.77   9.3*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.070       0.136       98.54   6.8*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.071       0.127      100.72   6.4*sigma

  Min. delta:    0.000
  Max. delta:    0.101
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  56  THR  HB , Angle CA-CB-HB, observed: 96.860, delta from target: 12.140

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.469
    Angle     :  1.719  12.140   4079  Z= 0.758
    Chirality :  0.361   4.650    176
    Planarity :  0.013   0.096    327
    Dihedral  : 14.454  85.665    769
    Min Nonbonded Distance : 1.749
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  6.57 %
      Favored  : 90.51 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  7.26 %
      Favored  : 87.90 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.26 (0.65), residues: 137
    helix: -1.09 (0.50), residues: 66
    sheet:  None (None), residues: 0
    loop : -1.89 (0.78), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.006   HIS A 135 
   PHE   0.084   0.022   PHE A  45 
   TYR   0.228   0.036   TYR A  50 
   ARG   0.053   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.006   HIS A 135 
   PHE   0.055   0.023   PHE A  45 
   TYR   0.185   0.039   TYR A  50 
   ARG   0.006   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.92 %
                favored =  90.51 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     1
  Clashscore            =   4.96
  RMS(bonds)            =   0.0090
  RMS(angles)           =   1.72
  MolProbity score      =   2.32

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.042 (Z=  2.595)
  Mean delta:    0.013 (Z=  0.669)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.50     5.10  1.00e+00  2.60e+01   5.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.04     4.56  1.00e+00  2.08e+01   4.6*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    9.534 (Z=  5.100)
  Mean delta:    1.929 (Z=  1.047)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00  -153.49   -26.51  5.00e+00  2.81e+01   5.3*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   157.62    22.38  5.00e+00  2.00e+01   4.5*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   159.00    21.00  5.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.059
  Max. delta:   66.571
  Mean delta:   15.101

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.329
  Mean delta:    0.091

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.153       0.282      471.07  14.1*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.075       0.143      111.52   7.1*sigma

  Min. delta:    0.000
  Max. delta:    0.160
  Mean delta:    0.021

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.042   2242  Z= 0.476
    Angle     :  1.746   9.534   4079  Z= 0.773
    Chirality :  0.091   0.329    176
    Planarity :  0.015   0.142    327
    Dihedral  : 13.475  89.741    769
    Min Nonbonded Distance : 1.456
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  : 10.22 %
      Favored  : 89.05 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  7.26 %
      Favored  : 90.32 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.12 (0.67), residues: 137
    helix: -0.35 (0.59), residues: 62
    sheet:  None (None), residues: 0
    loop : -1.05 (0.72), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.005   HIS A 138 
   PHE   0.132   0.027   PHE A  67 
   TYR   0.342   0.036   TYR A 105 
   ARG   0.125   0.015   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.005   HIS A 138 
   PHE   0.075   0.023   PHE A  67 
   TYR   0.282   0.041   TYR A 105 
   ARG   0.011   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   0.73 %
                favored =  89.05 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     1
  Clashscore            =   1.35
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.75
  MolProbity score      =   1.73

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.664)
  Mean delta:    0.013 (Z=  0.663)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.64     5.56  1.30e+00  1.83e+01   4.3*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.34     4.26  1.00e+00  1.81e+01   4.3*sigma
   A  29  ASP  CA
   A  29  ASP  CB
   A  29  ASP  CG        112.60   116.83    -4.23  1.00e+00  1.79e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.953 (Z=  4.279)
  Mean delta:    1.957 (Z=  1.086)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -154.42   -25.58  5.00e+00  2.62e+01   5.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   156.90    23.10  5.00e+00  2.14e+01   4.6*sigma
   A 111  TYR  CA
   A 111  TYR  C
   A 112  VAL  N
   A 112  VAL  CA        180.00  -156.95   -23.05  5.00e+00  2.12e+01   4.6*sigma

  Min. delta:    0.020
  Max. delta:   87.524
  Mean delta:   17.028

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.256
  Mean delta:    0.093

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.088       0.153      154.13   7.6*sigma
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.072       0.111       90.44   5.6*sigma

  Min. delta:    0.000
  Max. delta:    0.088
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.472
    Angle     :  1.783   9.002   4079  Z= 0.799
    Chirality :  0.093   0.256    176
    Planarity :  0.013   0.089    327
    Dihedral  : 14.494  87.524    769
    Min Nonbonded Distance : 1.744
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.84 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  3.23 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.92 (0.66), residues: 137
    helix: -1.25 (0.48), residues: 70
    sheet:  None (None), residues: 0
    loop : -1.19 (0.82), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A 138 
   PHE   0.166   0.036   PHE A  15 
   TYR   0.181   0.029   TYR A  50 
   ARG   0.049   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A 138 
   PHE   0.111   0.037   PHE A  15 
   TYR   0.153   0.033   TYR A  50 
   ARG   0.009   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.549)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.625 (Z=  1.363)
  Mean delta:    0.378 (Z=  0.207)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   78.013
  Mean delta:   22.792

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.094
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.045
    Angle     :  0.980   4.839   4077  Z= 0.342
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 17.597  78.013    768
    Min Nonbonded Distance : 1.476
  
  Molprobity Statistics.
    All-atom Clashscore : 25.71
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  : 18.98 %
      Favored  : 76.64 %
    Rotamer:
      Outliers : 25.81 %
      Allowed  : 20.97 %
      Favored  : 53.23 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -7.22 (0.36), residues: 137
    helix: -4.32 (0.29), residues: 67
    sheet:  None (None), residues: 0
    loop : -5.49 (0.41), residues: 70
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.001   0.000   PHE A  45 
   TYR   0.003   0.001   TYR A  68 
   ARG   0.001   0.000   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   TYR A  68 
   ARG   0.000   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.563)
  Mean delta:    0.001 (Z=  0.063)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.631 (Z=  1.383)
  Mean delta:    0.376 (Z=  0.206)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   87.232
  Mean delta:   22.470

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.095
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.046
    Angle     :  0.979   4.841   4077  Z= 0.342
    Chirality :  0.035   0.095    176
    Planarity :  0.000   0.001    326
    Dihedral  : 17.532  87.232    768
    Min Nonbonded Distance : 1.489
  
  Molprobity Statistics.
    All-atom Clashscore : 22.10
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  : 16.79 %
      Favored  : 76.64 %
    Rotamer:
      Outliers : 16.94 %
      Allowed  : 17.74 %
      Favored  : 65.32 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -7.15 (0.40), residues: 137
    helix: -3.98 (0.38), residues: 66
    sheet:  None (None), residues: 0
    loop : -5.78 (0.39), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.003   0.001   TYR A  91 
   ARG   0.001   0.000   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   TYR A  81 
   ARG   0.000   0.000   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  91.97 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     1
  Clashscore            =   7.66
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.78
  MolProbity score      =   2.20

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 128  MET  N
   A 128  MET  CA          1.46     1.55    -0.09  1.90e-02  2.44e+01   4.9*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.52    -0.07  1.60e-02  2.01e+01   4.5*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.094 (Z=  4.940)
  Mean delta:    0.015 (Z=  0.808)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   137.39   -26.09  2.30e+00  1.29e+02  11.3*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   107.64    14.06  1.80e+00  6.10e+01   7.8*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   135.41   -13.71  1.80e+00  5.80e+01   7.6*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   133.92   -12.22  1.80e+00  4.61e+01   6.8*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   133.44   -11.74  1.80e+00  4.26e+01   6.5*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  C         111.00   128.52   -17.52  2.80e+00  3.91e+01   6.3*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    98.54    11.56  1.90e+00  3.70e+01   6.1*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   132.41   -10.71  1.80e+00  3.54e+01   6.0*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   132.36   -10.66  1.80e+00  3.51e+01   5.9*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   120.48    -9.98  1.70e+00  3.45e+01   5.9*sigma
   A 122  ILE  C
   A 122  ILE  CA
   A 122  ILE  CB        111.60   123.24   -11.64  2.00e+00  3.39e+01   5.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   130.53    -9.73  1.70e+00  3.28e+01   5.7*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   124.18   -10.28  1.80e+00  3.26e+01   5.7*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   104.91    11.29  2.00e+00  3.18e+01   5.6*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   111.57    10.13  1.80e+00  3.17e+01   5.6*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   131.78   -10.08  1.80e+00  3.14e+01   5.6*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.00    -5.40  1.00e+00  2.92e+01   5.4*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   131.40    -9.70  1.80e+00  2.91e+01   5.4*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   117.93    -5.33  1.00e+00  2.84e+01   5.3*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.21    -9.51  1.80e+00  2.79e+01   5.3*sigma
   A 116  ASP  C
   A 116  ASP  CA
   A 116  ASP  CB        110.10   120.08    -9.98  1.90e+00  2.76e+01   5.3*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   120.06    -9.96  1.90e+00  2.75e+01   5.2*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.02   -10.42  2.00e+00  2.71e+01   5.2*sigma
   A  96  GLY  O
   A  96  GLY  C
   A  97  SER  N         123.00   114.92     8.08  1.60e+00  2.55e+01   5.1*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   102.95     8.55  1.70e+00  2.53e+01   5.0*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   101.92     9.48  1.90e+00  2.49e+01   5.0*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   102.15     8.35  1.70e+00  2.41e+01   4.9*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG2       110.50   118.81    -8.31  1.70e+00  2.39e+01   4.9*sigma
   A  86  ILE  N
   A  86  ILE  CA
   A  86  ILE  CB        111.50   119.67    -8.17  1.70e+00  2.31e+01   4.8*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   119.20    -9.10  1.90e+00  2.29e+01   4.8*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  CB        110.50   102.38     8.12  1.70e+00  2.28e+01   4.8*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   105.33     6.67  1.40e+00  2.27e+01   4.8*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   130.21    -8.51  1.80e+00  2.24e+01   4.7*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   106.84     9.36  2.00e+00  2.19e+01   4.7*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   118.96    -8.86  1.90e+00  2.18e+01   4.7*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    98.06    12.94  2.80e+00  2.14e+01   4.6*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   130.01    -8.31  1.80e+00  2.13e+01   4.6*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30   100.09     9.21  2.00e+00  2.12e+01   4.6*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   118.09    -7.69  1.70e+00  2.05e+01   4.5*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   107.34     8.86  2.00e+00  1.96e+01   4.4*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   129.33    -7.63  1.80e+00  1.79e+01   4.2*sigma
   A 118  ASP  N
   A 118  ASP  CA
   A 118  ASP  C         111.00    99.37    11.63  2.80e+00  1.72e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.54     4.06  1.00e+00  1.65e+01   4.1*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.06    -5.66  1.40e+00  1.64e+01   4.0*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   128.97    -7.27  1.80e+00  1.63e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:   26.085 (Z= 11.341)
  Mean delta:    2.793 (Z=  1.481)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00    55.40   124.60  5.00e+00  6.21e+02  24.9*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    67.83   112.17  5.00e+00  5.03e+02  22.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00    90.13    89.87  5.00e+00  3.23e+02  18.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   -91.09   -88.91  5.00e+00  3.16e+02  17.8*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   -99.80   -80.20  5.00e+00  2.57e+02  16.0*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -104.89   -75.11  5.00e+00  2.26e+02  15.0*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   111.37    68.63  5.00e+00  1.88e+02  13.7*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   113.20    66.80  5.00e+00  1.78e+02  13.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -116.11   -63.89  5.00e+00  1.63e+02  12.8*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   119.06    60.94  5.00e+00  1.49e+02  12.2*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   120.08    59.92  5.00e+00  1.44e+02  12.0*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   120.85    59.15  5.00e+00  1.40e+02  11.8*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -125.02   -54.98  5.00e+00  1.21e+02  11.0*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -128.15   -51.85  5.00e+00  1.08e+02  10.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -128.49   -51.51  5.00e+00  1.06e+02  10.3*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA          0.00   -42.13    42.13  5.00e+00  7.10e+01   8.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   138.35    41.65  5.00e+00  6.94e+01   8.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   147.39    32.61  5.00e+00  4.25e+01   6.5*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   148.15    31.85  5.00e+00  4.06e+01   6.4*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   148.98    31.02  5.00e+00  3.85e+01   6.2*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   149.83    30.17  5.00e+00  3.64e+01   6.0*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   150.93    29.07  5.00e+00  3.38e+01   5.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   154.30    25.70  5.00e+00  2.64e+01   5.1*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   154.39    25.61  5.00e+00  2.62e+01   5.1*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -154.65   -25.35  5.00e+00  2.57e+01   5.1*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   154.67    25.33  5.00e+00  2.57e+01   5.1*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   158.56    21.44  5.00e+00  1.84e+01   4.3*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   159.88    20.12  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.018
  Max. delta:  124.597
  Mean delta:   21.945

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.95     5.48  2.00e-01  7.50e+02  27.4*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.92     5.43  2.00e-01  7.37e+02  27.1*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.89     5.40  2.00e-01  7.30e+02  27.0*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.77     5.28  2.00e-01  6.97e+02  26.4*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.51     5.15  2.00e-01  6.64e+02  25.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.64     5.08  2.00e-01  6.45e+02  25.4*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.53     5.04  2.00e-01  6.36e+02  25.2*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.48     4.99  2.00e-01  6.23e+02  25.0*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.43     4.98  2.00e-01  6.19e+02  24.9*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.30     4.94  2.00e-01  6.11e+02  24.7*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.38     4.89  2.00e-01  5.99e+02  24.5*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -2.15     4.66  2.00e-01  5.42e+02  23.3*sigma
   A 116  ASP  CA
   A 116  ASP  N
   A 116  ASP  C
   A 116  ASP  CB          2.51    -2.03     4.54  2.00e-01  5.16e+02  22.7*sigma
   A 130  SER  CA
   A 130  SER  N
   A 130  SER  C
   A 130  SER  CB          2.51    -2.01     4.52  2.00e-01  5.11e+02  22.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.80     4.23  2.00e-01  4.48e+02  21.2*sigma

  Min. delta:    0.001
  Max. delta:    5.477
  Mean delta:    1.466

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.108       0.207      235.32  10.4*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.051       0.096       51.23   4.8*sigma

  Min. delta:    0.000
  Max. delta:    0.125
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  86  ILE  HA , Angle N-CA-HA, observed: 97.609, delta from target: 12.391
   A  51  ILE  HA , Angle CB-CA-HA, observed: 95.656, delta from target: 13.344
   A  93  LEU  HA , Angle N-CA-HA, observed: 96.488, delta from target: 13.512
   A 122  ILE  HA , Angle C-CA-HA, observed: 91.163, delta from target: 17.837
   A  93  LEU  HA , Angle CB-CA-HA, observed: 127.409, delta from target: -18.409

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.094   2242  Z= 0.575
    Angle     :  2.409  26.085   4079  Z= 1.070
    Chirality :  1.466   5.477    176
    Planarity :  0.014   0.125    327
    Dihedral  : 17.410 124.597    769
    Min Nonbonded Distance : 1.720
  
  Molprobity Statistics.
    All-atom Clashscore : 12.62
    Ramachandran Plot:
      Outliers : 13.87 %
      Allowed  :  7.30 %
      Favored  : 78.83 %
    Rotamer:
      Outliers :  8.87 %
      Allowed  :  8.06 %
      Favored  : 83.06 %
    Cbeta Deviations : 15.91 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 28.57 %
      Twisted General : 14.50 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.23 (0.67), residues: 137
    helix: -1.23 (0.57), residues: 63
    sheet:  None (None), residues: 0
    loop : -3.10 (0.72), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.054   0.013   PHE A  15 
   TYR   0.244   0.024   TYR A  91 
   ARG   0.018   0.003   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.039   0.014   PHE A  15 
   TYR   0.207   0.030   TYR A  91 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   4.38 %
                favored =  76.64 %
  Rotamer outliers      =  25.81 %
  C-beta deviations     =     0
  Clashscore            =  25.71
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.75

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Ramachandran outliers =   6.57 %
                favored =  76.64 %
  Rotamer outliers      =  16.94 %
  C-beta deviations     =     0
  Clashscore            =  22.10
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.55

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =  13.87 %
                favored =  78.83 %
  Rotamer outliers      =   8.87 %
  C-beta deviations     =    21
  Clashscore            =  12.62
  RMS(bonds)            =   0.0110
  RMS(angles)           =   2.41
  MolProbity score      =   3.08

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.579)
  Mean delta:    0.001 (Z=  0.063)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.605 (Z=  1.343)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   78.804
  Mean delta:   22.935

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.096
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.046
    Angle     :  0.980   4.829   4077  Z= 0.341
    Chirality :  0.035   0.096    176
    Planarity :  0.000   0.001    326
    Dihedral  : 17.915  78.804    768
    Min Nonbonded Distance : 1.528
  
  Molprobity Statistics.
    All-atom Clashscore : 23.00
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  : 16.79 %
      Favored  : 78.83 %
    Rotamer:
      Outliers : 24.19 %
      Allowed  : 10.48 %
      Favored  : 65.32 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.98 (0.41), residues: 137
    helix: -4.37 (0.29), residues: 66
    sheet:  None (None), residues: 0
    loop : -5.09 (0.51), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.002   0.001   PHE A  15 
   TYR   0.002   0.001   TYR A 105 
   ARG   0.001   0.000   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.001   0.000   PHE A  67 
   TYR   0.001   0.000   TYR A 105 
   ARG   0.000   0.000   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  72  ASN

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   4.38 %
                favored =  78.83 %
  Rotamer outliers      =  24.19 %
  C-beta deviations     =     0
  Clashscore            =  23.00
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.66

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.58    -0.12  1.60e-02  6.10e+01   7.8*sigma
   A 123  GLU  N
   A 123  GLU  CA          1.46     1.36     0.10  1.90e-02  2.81e+01   5.3*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.63    -0.10  2.10e-02  2.32e+01   4.8*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.43     0.10  2.10e-02  2.20e+01   4.7*sigma

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.125 (Z=  7.812)
  Mean delta:    0.017 (Z=  0.893)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   141.89   -20.19  1.80e+00  1.26e+02  11.2*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   127.60   -17.50  1.90e+00  8.48e+01   9.2*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   105.19    16.51  1.80e+00  8.41e+01   9.2*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   100.19    16.01  2.00e+00  6.41e+01   8.0*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   100.98    15.22  2.00e+00  5.79e+01   7.6*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   123.20   -12.80  1.70e+00  5.66e+01   7.5*sigma
   A  78  ILE  CB
   A  78  ILE  CG1
   A  78  ILE  CD1       113.80   129.38   -15.58  2.10e+00  5.50e+01   7.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.84   -13.14  1.80e+00  5.33e+01   7.3*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    99.21    12.29  1.70e+00  5.22e+01   7.2*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   123.54   -13.44  1.90e+00  5.00e+01   7.1*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   129.44   -18.44  2.80e+00  4.34e+01   6.6*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   129.13   -12.93  2.00e+00  4.18e+01   6.5*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   110.24    11.46  1.80e+00  4.06e+01   6.4*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG2       110.50   121.31   -10.81  1.70e+00  4.05e+01   6.4*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   121.16   -10.66  1.70e+00  3.94e+01   6.3*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   118.81    -6.21  1.00e+00  3.85e+01   6.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   104.08    12.12  2.00e+00  3.67e+01   6.1*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   132.23    -9.23  1.60e+00  3.33e+01   5.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.95   -11.35  2.00e+00  3.22e+01   5.7*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   123.66    -9.76  1.80e+00  2.94e+01   5.4*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   111.96     9.74  1.80e+00  2.93e+01   5.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   105.40    10.80  2.00e+00  2.92e+01   5.4*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.36    -9.66  1.80e+00  2.88e+01   5.4*sigma
   A  39  LEU  C
   A  39  LEU  CA
   A  39  LEU  CB        110.10   120.29   -10.19  1.90e+00  2.88e+01   5.4*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   130.98    -9.28  1.80e+00  2.66e+01   5.2*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    96.83    14.17  2.80e+00  2.56e+01   5.1*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   101.81     9.79  2.00e+00  2.40e+01   4.9*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   131.25    -6.85  1.40e+00  2.40e+01   4.9*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  C         111.00    97.57    13.43  2.80e+00  2.30e+01   4.8*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O         120.80   128.94    -8.14  1.70e+00  2.29e+01   4.8*sigma
   A 123  GLU  O
   A 123  GLU  C
   A 124  ALA  N         123.00   130.59    -7.59  1.60e+00  2.25e+01   4.7*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG1       110.40   118.29    -7.89  1.70e+00  2.15e+01   4.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   128.55    -7.75  1.70e+00  2.08e+01   4.6*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  C         111.00   123.66   -12.66  2.80e+00  2.05e+01   4.5*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG2       110.50   118.04    -7.54  1.70e+00  1.97e+01   4.4*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.00    -4.40  1.00e+00  1.93e+01   4.4*sigma
   A  52  PRO  C
   A  52  PRO  CA
   A  52  PRO  CB        110.10   118.43    -8.33  1.90e+00  1.92e+01   4.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O         120.80   113.57     7.23  1.70e+00  1.81e+01   4.3*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   129.35    -7.65  1.80e+00  1.81e+01   4.3*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   129.33    -7.63  1.80e+00  1.80e+01   4.2*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   129.29    -7.59  1.80e+00  1.78e+01   4.2*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   116.79    -4.19  1.00e+00  1.75e+01   4.2*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   103.62     7.78  1.90e+00  1.67e+01   4.1*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.91     5.29  1.30e+00  1.66e+01   4.1*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N         116.20   108.06     8.14  2.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   20.189 (Z= 11.216)
  Mean delta:    2.916 (Z=  1.566)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    50.76   129.24  5.00e+00  6.68e+02  25.8*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00    69.86   110.14  5.00e+00  4.85e+02  22.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   -73.34  -106.66  5.00e+00  4.55e+02  21.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   -80.50   -99.50  5.00e+00  3.96e+02  19.9*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   -90.03   -89.97  5.00e+00  3.24e+02  18.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -106.22   -73.78  5.00e+00  2.18e+02  14.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   108.70    71.30  5.00e+00  2.03e+02  14.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00  -109.93   -70.07  5.00e+00  1.96e+02  14.0*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -121.63   -58.37  5.00e+00  1.36e+02  11.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   126.97    53.03  5.00e+00  1.13e+02  10.6*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -129.95   -50.05  5.00e+00  1.00e+02  10.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -140.13   -39.87  5.00e+00  6.36e+01   8.0*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -141.31   -38.69  5.00e+00  5.99e+01   7.7*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -144.75   -35.25  5.00e+00  4.97e+01   7.1*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -145.83   -34.17  5.00e+00  4.67e+01   6.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -149.07   -30.93  5.00e+00  3.83e+01   6.2*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   154.55    25.45  5.00e+00  2.59e+01   5.1*sigma
   A 111  TYR  CA
   A 111  TYR  C
   A 112  VAL  N
   A 112  VAL  CA        180.00   155.13    24.87  5.00e+00  2.47e+01   5.0*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   159.51    20.49  5.00e+00  1.68e+01   4.1*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   159.84    20.16  5.00e+00  1.63e+01   4.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00  -159.96   -20.04  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.021
  Max. delta:  129.238
  Mean delta:   21.020

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.41     5.06  2.00e-01  6.39e+02  25.3*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  C
   A  52  PRO  CB          2.72    -2.30     5.02  2.00e-01  6.30e+02  25.1*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.57     5.01  2.00e-01  6.28e+02  25.1*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -2.02     4.53  2.00e-01  5.12e+02  22.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.57     4.00  2.00e-01  4.00e+02  20.0*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51     0.94     1.57  2.00e-01  6.16e+01   7.8*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.28     1.23  2.00e-01  3.75e+01   6.1*sigma

  Min. delta:    0.003
  Max. delta:    5.056
  Mean delta:    0.827

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O
   A 127  ARG  N             0.051       0.088       25.81   4.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O
   A  91  TYR  N             0.048       0.083       23.15   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.092
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  90  SER  HA , Angle CB-CA-HA, observed: 96.694, delta from target: 12.306
   A  52  PRO  HA , Angle C-CA-HA, observed: 96.398, delta from target: 12.602
   A 127  ARG  HA , Angle CB-CA-HA, observed: 121.658, delta from target: -12.658
   A  51  ILE  HA , Angle C-CA-HA, observed: 96.323, delta from target: 12.677
   A  79  LYS  HA , Angle C-CA-HA, observed: 122.340, delta from target: -13.340
   A  51  ILE  HA , Angle CB-CA-HA, observed: 94.527, delta from target: 14.473
   A 126  VAL  HB , Angle CA-CB-HB, observed: 92.023, delta from target: 16.977
   A 131  ILE  HA , Angle C-CA-HA, observed: 91.033, delta from target: 17.967
   A 127  ARG  HA , Angle N-CA-HA, observed: 88.686, delta from target: 21.314
   A 127  ARG  HA , Angle C-CA-HA, observed: 87.151, delta from target: 21.849
   A 128  MET  HA , Angle CB-CA-HA, observed: 86.365, delta from target: 22.635
   A 128  MET  HA , Angle C-CA-HA, observed: 84.100, delta from target: 25.900

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.125   2242  Z= 0.636
    Angle     :  2.573  25.900   4079  Z= 1.142
    Chirality :  0.827   5.056    176
    Planarity :  0.011   0.092    327
    Dihedral  : 17.079 129.238    769
    Min Nonbonded Distance : 1.610
  
  Molprobity Statistics.
    All-atom Clashscore : 12.62
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  :  9.49 %
      Favored  : 82.48 %
    Rotamer:
      Outliers :  8.87 %
      Allowed  :  5.65 %
      Favored  : 85.48 %
    Cbeta Deviations :  9.09 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 11.45 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.08 (0.69), residues: 137
    helix: -1.69 (0.57), residues: 61
    sheet:  None (None), residues: 0
    loop : -2.41 (0.76), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A 136 
   PHE   0.068   0.018   PHE A  45 
   TYR   0.099   0.014   TYR A  12 
   ARG   0.023   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A 136 
   PHE   0.044   0.017   PHE A  45 
   TYR   0.083   0.016   TYR A  12 
   ARG   0.002   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   8.03 %
                favored =  82.48 %
  Rotamer outliers      =   8.87 %
  C-beta deviations     =    12
  Clashscore            =  12.62
  RMS(bonds)            =   0.0121
  RMS(angles)           =   2.57
  MolProbity score      =   3.03

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  91  TYR  N
   A  91  TYR  CA          1.46     1.59    -0.14  1.90e-02  5.14e+01   7.2*sigma
   A  92  THR  CB
   A  92  THR  OG1         1.43     1.33     0.10  1.60e-02  4.20e+01   6.5*sigma
   A  90  SER  C
   A  91  TYR  N           1.33     1.42    -0.09  1.40e-02  3.83e+01   6.2*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.57    -0.11  1.90e-02  3.47e+01   5.9*sigma
   A  93  LEU  CB
   A  93  LEU  CG          1.53     1.65    -0.12  2.00e-02  3.39e+01   5.8*sigma
   A  91  TYR  CA
   A  91  TYR  C           1.52     1.64    -0.11  2.10e-02  2.94e+01   5.4*sigma
   A  98  SER  CA
   A  98  SER  C           1.52     1.63    -0.11  2.10e-02  2.64e+01   5.1*sigma
   A  77  ILE  C
   A  78  ILE  N           1.33     1.26     0.07  1.40e-02  2.60e+01   5.1*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.63    -0.11  2.10e-02  2.50e+01   5.0*sigma
   A  90  SER  CA
   A  90  SER  C           1.52     1.62    -0.10  2.10e-02  2.20e+01   4.7*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.136 (Z=  7.171)
  Mean delta:    0.018 (Z=  0.939)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   146.85   -36.35  1.70e+00  4.57e+02  21.4*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   138.35   -27.85  1.70e+00  2.68e+02  16.4*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   139.42   -27.82  2.00e+00  1.94e+02  13.9*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   127.73   -17.23  1.70e+00  1.03e+02  10.1*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   139.80   -18.10  1.80e+00  1.01e+02  10.1*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   139.25   -17.55  1.80e+00  9.51e+01   9.8*sigma
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   137.66   -15.96  1.80e+00  7.86e+01   8.9*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   136.45   -14.75  1.80e+00  6.72e+01   8.2*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   135.89   -14.19  1.80e+00  6.22e+01   7.9*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   126.08   -14.48  2.00e+00  5.24e+01   7.2*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD1       110.70   132.11   -21.41  3.00e+00  5.09e+01   7.1*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  C         111.00   129.30   -18.30  2.80e+00  4.27e+01   6.5*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   124.29   -12.69  2.00e+00  4.02e+01   6.3*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   132.55   -10.85  1.80e+00  3.64e+01   6.0*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   101.02     8.58  1.50e+00  3.27e+01   5.7*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O         120.80   111.21     9.59  1.70e+00  3.19e+01   5.6*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   127.37   -11.17  2.00e+00  3.12e+01   5.6*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   125.11    -8.21  1.50e+00  3.00e+01   5.5*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.40    -9.70  1.80e+00  2.90e+01   5.4*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.98    -5.38  1.00e+00  2.89e+01   5.4*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   131.19    -9.49  1.80e+00  2.78e+01   5.3*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  CB        111.50   102.61     8.89  1.70e+00  2.73e+01   5.2*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00   124.71   -13.71  2.80e+00  2.40e+01   4.9*sigma
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        121.70   130.36    -8.66  1.80e+00  2.32e+01   4.8*sigma
   A  93  LEU  CA
   A  93  LEU  CB
   A  93  LEU  CG        116.30   100.13    16.17  3.50e+00  2.13e+01   4.6*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  CB        110.50   102.88     7.62  1.70e+00  2.01e+01   4.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.49     5.71  1.30e+00  1.93e+01   4.4*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   118.31    -8.21  1.90e+00  1.87e+01   4.3*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  C         111.00   123.09   -12.09  2.80e+00  1.86e+01   4.3*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.35    -5.95  1.40e+00  1.80e+01   4.2*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   118.01    -7.91  1.90e+00  1.73e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   114.23     7.47  1.80e+00  1.72e+01   4.2*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   117.31    -6.81  1.70e+00  1.61e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   36.351 (Z= 21.383)
  Mean delta:    3.047 (Z=  1.621)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   -49.36  -130.64  5.00e+00  6.83e+02  26.1*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00    77.19   102.81  5.00e+00  4.23e+02  20.6*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -121.65   -58.35  5.00e+00  1.36e+02  11.7*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -134.86   -45.14  5.00e+00  8.15e+01   9.0*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -140.06   -39.94  5.00e+00  6.38e+01   8.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -147.75   -32.25  5.00e+00  4.16e+01   6.5*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   149.63    30.37  5.00e+00  3.69e+01   6.1*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   153.02    26.98  5.00e+00  2.91e+01   5.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -153.54   -26.46  5.00e+00  2.80e+01   5.3*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   159.15    20.85  5.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.021
  Max. delta:  130.644
  Mean delta:   17.988

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.59     5.10  2.00e-01  6.49e+02  25.5*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.51     5.02  2.00e-01  6.29e+02  25.1*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.17     4.69  2.00e-01  5.51e+02  23.5*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -1.96     4.47  2.00e-01  5.00e+02  22.4*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -1.74     4.39  2.00e-01  4.82e+02  21.9*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.52     3.96  2.00e-01  3.91e+02  19.8*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.74     3.17  2.00e-01  2.52e+02  15.9*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55     0.98     1.57  2.00e-01  6.18e+01   7.9*sigma
   A  93  LEU  CG
   A  93  LEU  CB
   A  93  LEU  CD1
   A  93  LEU  CD2        -2.59    -1.42    -1.17  2.00e-01  3.41e+01   5.8*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51     1.66     0.85  2.00e-01  1.81e+01   4.3*sigma

  Min. delta:    0.001
  Max. delta:    5.096
  Mean delta:    0.912

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.048       0.091       46.93   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.063
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  83  THR  HA , Angle N-CA-HA, observed: 97.555, delta from target: 12.445
   A  91  TYR  HA , Angle CB-CA-HA, observed: 121.696, delta from target: -12.696
   A  93  LEU  HG , Angle CD1-CG-HG, observed: 95.090, delta from target: 12.910
   A  91  TYR  HA , Angle C-CA-HA, observed: 94.337, delta from target: 14.663
   A  74  ASP  HA , Angle C-CA-HA, observed: 92.817, delta from target: 16.183
   A  78  ILE  HA , Angle CB-CA-HA, observed: 92.009, delta from target: 16.991
   A  92  THR  HA , Angle N-CA-HA, observed: 92.978, delta from target: 17.022
   A  93  LEU  HG , Angle CD2-CG-HG, observed: 126.255, delta from target: -18.255
   A  91  TYR  HA , Angle N-CA-HA, observed: 91.245, delta from target: 18.755
   A  92  THR  HB , Angle CA-CB-HB, observed: 87.453, delta from target: 21.547
   A  51  ILE  HA , Angle C-CA-HA, observed: 86.190, delta from target: 22.810
   A  78  ILE  HB , Angle CG1-CB-HB, observed: 134.774, delta from target: -25.774
   A  78  ILE  HA , Angle C-CA-HA, observed: 82.376, delta from target: 26.624
   A  78  ILE  HA , Angle N-CA-HA, observed: 136.647, delta from target: -26.647
   A  93  LEU  HA , Angle CB-CA-HA, observed: 82.207, delta from target: 26.793
   A  51  ILE  HA , Angle CB-CA-HA, observed: 81.877, delta from target: 27.123
   A  92  THR  HB , Angle CG2-CB-HB, observed: 80.184, delta from target: 27.816
   A  78  ILE  HB , Angle CA-CB-HB, observed: 80.321, delta from target: 28.679
   A  93  LEU  HG , Angle CB-CG-HG, observed: 79.514, delta from target: 29.486
   A  92  THR  HB , Angle OG1-CB-HB, observed: 148.082, delta from target: -39.082

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.136   2242  Z= 0.668
    Angle     :  2.929  39.082   4079  Z= 1.247
    Chirality :  0.912   5.096    176
    Planarity :  0.010   0.059    327
    Dihedral  : 14.866 130.644    769
    Min Nonbonded Distance : 1.372
  
  Molprobity Statistics.
    All-atom Clashscore : 14.43
    Ramachandran Plot:
      Outliers :  7.30 %
      Allowed  :  5.84 %
      Favored  : 86.86 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  6.45 %
      Favored  : 86.29 %
    Cbeta Deviations :  8.33 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 5.34 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.87 (0.64), residues: 137
    helix: -1.15 (0.49), residues: 81
    sheet:  None (None), residues: 0
    loop : -3.03 (0.79), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.023   0.006   PHE A  67 
   TYR   0.143   0.019   TYR A  50 
   ARG   0.033   0.006   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.013   0.005   PHE A  67 
   TYR   0.113   0.022   TYR A  50 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   7.30 %
                favored =  86.86 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    11
  Clashscore            =  14.43
  RMS(bonds)            =   0.0128
  RMS(angles)           =   2.93
  MolProbity score      =   2.94

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.64    -0.19  1.60e-02  1.37e+02  11.7*sigma
   A 127  ARG  C
   A 128  MET  N           1.33     1.22     0.11  1.40e-02  6.27e+01   7.9*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.60    -0.14  1.90e-02  5.63e+01   7.5*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.65    -0.13  2.10e-02  3.78e+01   6.2*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.65    -0.13  2.10e-02  3.61e+01   6.0*sigma
   A 127  ARG  CA
   A 127  ARG  C           1.52     1.42     0.11  2.10e-02  2.50e+01   5.0*sigma
   A  90  SER  N
   A  90  SER  CA          1.46     1.55    -0.09  1.90e-02  2.38e+01   4.9*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     1.54    -0.09  1.90e-02  2.05e+01   4.5*sigma
   A  89  TYR  N
   A  89  TYR  CA          1.46     1.38     0.08  1.90e-02  1.77e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.004)
  Max. delta:    0.187 (Z= 11.683)
  Mean delta:    0.019 (Z=  1.007)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   143.24   -21.54  1.80e+00  1.43e+02  12.0*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   142.77   -21.07  1.80e+00  1.37e+02  11.7*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   141.70   -20.00  1.80e+00  1.23e+02  11.1*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   132.55   -18.65  1.80e+00  1.07e+02  10.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.73   -11.83  1.50e+00  6.22e+01   7.9*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   123.81   -13.31  1.70e+00  6.13e+01   7.8*sigma
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG2       110.50   123.67   -13.17  1.70e+00  6.00e+01   7.7*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   109.00    12.70  1.80e+00  4.98e+01   7.1*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   133.84   -12.14  1.80e+00  4.55e+01   6.7*sigma
   A  91  TYR  O
   A  91  TYR  C
   A  92  THR  N         123.00   112.24    10.76  1.60e+00  4.52e+01   6.7*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   109.98    11.72  1.80e+00  4.24e+01   6.5*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   122.46   -12.36  1.90e+00  4.23e+01   6.5*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   103.57    12.63  2.00e+00  3.99e+01   6.3*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   100.87    10.63  1.70e+00  3.91e+01   6.3*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   119.62    -9.12  1.50e+00  3.70e+01   6.1*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N         116.20   127.83   -11.63  2.00e+00  3.38e+01   5.8*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50   121.29    -9.79  1.70e+00  3.32e+01   5.8*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10    99.23    10.87  1.90e+00  3.27e+01   5.7*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   120.16    -9.66  1.70e+00  3.23e+01   5.7*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.78   -11.18  2.00e+00  3.13e+01   5.6*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   126.16   -15.16  2.80e+00  2.93e+01   5.4*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.42    -9.72  1.80e+00  2.92e+01   5.4*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   105.48    10.72  2.00e+00  2.87e+01   5.4*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   120.26   -10.16  1.90e+00  2.86e+01   5.3*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00   125.87   -14.87  2.80e+00  2.82e+01   5.3*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   112.34     9.36  1.80e+00  2.70e+01   5.2*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   119.93    -9.83  1.90e+00  2.68e+01   5.2*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG2       110.50   119.16    -8.66  1.70e+00  2.60e+01   5.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   101.94     8.56  1.70e+00  2.54e+01   5.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   106.18    10.02  2.00e+00  2.51e+01   5.0*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   125.00   -14.00  2.80e+00  2.50e+01   5.0*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N         116.20   126.02    -9.82  2.00e+00  2.41e+01   4.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.47    -4.87  1.00e+00  2.37e+01   4.9*sigma
   A  87  GLY  N
   A  87  GLY  CA
   A  87  GLY  C         113.30    99.48    13.82  2.90e+00  2.27e+01   4.8*sigma
   A  83  THR  N
   A  83  THR  CA
   A  83  THR  CB        111.50   119.30    -7.80  1.70e+00  2.10e+01   4.6*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   129.94    -8.24  1.80e+00  2.09e+01   4.6*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   118.14    -7.74  1.70e+00  2.07e+01   4.6*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   118.69    -8.59  1.90e+00  2.05e+01   4.5*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   107.16     9.04  2.00e+00  2.04e+01   4.5*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   118.14    -7.64  1.70e+00  2.02e+01   4.5*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O         120.80   128.39    -7.59  1.70e+00  1.99e+01   4.5*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   118.03    -7.53  1.70e+00  1.96e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.57     5.63  1.30e+00  1.88e+01   4.3*sigma
   A  86  ILE  N
   A  86  ILE  CA
   A  86  ILE  C         111.00    99.00    12.00  2.80e+00  1.84e+01   4.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.55     7.25  1.70e+00  1.82e+01   4.3*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG2       110.50   117.74    -7.24  1.70e+00  1.82e+01   4.3*sigma
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        121.70   129.35    -7.65  1.80e+00  1.81e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   21.541 (Z= 11.967)
  Mean delta:    2.995 (Z=  1.610)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    53.52   126.48  5.00e+00  6.40e+02  25.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    58.45   121.55  5.00e+00  5.91e+02  24.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    61.13   118.87  5.00e+00  5.65e+02  23.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    64.63   115.37  5.00e+00  5.32e+02  23.1*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    68.81   111.19  5.00e+00  4.95e+02  22.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -89.85   -90.15  5.00e+00  3.25e+02  18.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00    97.89    82.11  5.00e+00  2.70e+02  16.4*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   116.38    63.62  5.00e+00  1.62e+02  12.7*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   125.52    54.48  5.00e+00  1.19e+02  10.9*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -128.72   -51.28  5.00e+00  1.05e+02  10.3*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   134.19    45.81  5.00e+00  8.39e+01   9.2*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   135.92    44.08  5.00e+00  7.77e+01   8.8*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -136.61   -43.39  5.00e+00  7.53e+01   8.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   138.45    41.55  5.00e+00  6.91e+01   8.3*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -140.53   -39.47  5.00e+00  6.23e+01   7.9*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   142.62    37.38  5.00e+00  5.59e+01   7.5*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   150.30    29.70  5.00e+00  3.53e+01   5.9*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA          0.00   -29.50    29.50  5.00e+00  3.48e+01   5.9*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   150.70    29.30  5.00e+00  3.43e+01   5.9*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   158.69    21.31  5.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.011
  Max. delta:  126.478
  Mean delta:   21.611

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.05     5.56  2.00e-01  7.74e+02  27.8*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.48     5.13  2.00e-01  6.57e+02  25.6*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -2.43     4.94  2.00e-01  6.11e+02  24.7*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -2.40     4.91  2.00e-01  6.02e+02  24.5*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.35     4.86  2.00e-01  5.90e+02  24.3*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.20     4.71  2.00e-01  5.55e+02  23.6*sigma
   A 130  SER  CA
   A 130  SER  N
   A 130  SER  C
   A 130  SER  CB          2.51    -2.18     4.69  2.00e-01  5.49e+02  23.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.05     4.60  2.00e-01  5.29e+02  23.0*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -1.91     4.44  2.00e-01  4.92e+02  22.2*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -1.14     3.57  2.00e-01  3.19e+02  17.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.01     3.44  2.00e-01  2.96e+02  17.2*sigma
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51     1.55     0.96  2.00e-01  2.29e+01   4.8*sigma

  Min. delta:    0.001
  Max. delta:    5.565
  Mean delta:    1.177

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.067       0.117       90.60   5.9*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O
   A 127  ARG  N             0.061       0.105       37.14   5.3*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.050       0.094       49.98   4.7*sigma

  Min. delta:    0.000
  Max. delta:    0.067
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="THR A  92  conformer  : H 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 131  ILE  HA , Angle C-CA-HA, observed: 96.958, delta from target: 12.042
   A 130  SER  HA , Angle N-CA-HA, observed: 97.865, delta from target: 12.135
   A 130  SER  HA , Angle C-CA-HA, observed: 96.729, delta from target: 12.271
   A  83  THR  HA , Angle CB-CA-HA, observed: 96.619, delta from target: 12.381
   A  78  ILE  HA , Angle N-CA-HA, observed: 97.554, delta from target: 12.446
   A  86  ILE  HB , Angle CG1-CB-HB, observed: 121.596, delta from target: -12.596
   A  74  ASP  HA , Angle C-CA-HA, observed: 96.394, delta from target: 12.606
   A  92  THR  HB , Angle CA-CB-HB, observed: 96.339, delta from target: 12.661
   A 128  MET  HA , Angle C-CA-HA, observed: 95.216, delta from target: 14.784
   A 122  ILE  HA , Angle N-CA-HA, observed: 95.152, delta from target: 14.848
   A 129  ARG  HA , Angle N-CA-HA, observed: 93.412, delta from target: 16.588
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.749, delta from target: 17.251
   A  51  ILE  HA , Angle CB-CA-HA, observed: 90.746, delta from target: 18.254
   A  90  SER  HA , Angle N-CA-HA, observed: 91.220, delta from target: 18.780
   A 122  ILE  HA , Angle C-CA-HA, observed: 83.874, delta from target: 25.126

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.187   2241  Z= 0.717
    Angle     :  2.620  25.126   4077  Z= 1.169
    Chirality :  1.177   5.565    176
    Planarity :  0.011   0.063    326
    Dihedral  : 17.147 126.478    768
    Min Nonbonded Distance : 1.401
  
  Molprobity Statistics.
    All-atom Clashscore : 19.40
    Ramachandran Plot:
      Outliers :  8.76 %
      Allowed  : 12.41 %
      Favored  : 78.83 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  5.65 %
      Favored  : 87.10 %
    Cbeta Deviations : 13.64 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 12.21 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.49 (0.65), residues: 137
    helix: -1.55 (0.53), residues: 63
    sheet:  None (None), residues: 0
    loop : -3.14 (0.73), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.004   HIS A  43 
   PHE   0.038   0.009   PHE A  45 
   TYR   0.141   0.018   TYR A  12 
   ARG   0.052   0.009   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.004   HIS A  43 
   PHE   0.027   0.009   PHE A  45 
   TYR   0.117   0.021   TYR A  12 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.642)
  Mean delta:    0.013 (Z=  0.689)

                        ----------Bond angles----------                        

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 125  LYS  CA
   A 125  LYS  C           1.52     1.43     0.09  2.10e-02  1.96e+01   4.4*sigma
   A 123  GLU  N
   A 123  GLU  CA          1.46     1.54    -0.08  1.90e-02  1.94e+01   4.4*sigma
   A 125  LYS  C
   A 126  VAL  N           1.33     1.27     0.06  1.40e-02  1.69e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.093 (Z=  4.426)
  Mean delta:    0.015 (Z=  0.768)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   134.31   -12.61  1.80e+00  4.91e+01   7.0*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   132.59   -10.89  1.80e+00  3.66e+01   6.0*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.98     4.62  1.00e+00  2.13e+01   4.6*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   118.49    -8.39  1.90e+00  1.95e+01   4.4*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  CD2       131.20   125.70     5.50  1.30e+00  1.79e+01   4.2*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   108.37     4.23  1.00e+00  1.79e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   12.609 (Z=  7.005)
  Mean delta:    2.015 (Z=  1.098)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -144.68   -35.32  5.00e+00  4.99e+01   7.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -149.24   -30.76  5.00e+00  3.78e+01   6.2*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -158.80   -21.20  5.00e+00  1.80e+01   4.2*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -159.04   -20.96  5.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.075
  Max. delta:   90.967
  Mean delta:   18.387

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.15     4.66  2.00e-01  5.42e+02  23.3*sigma
   A  75  GLU  CA
   A  75  GLU  N
   A  75  GLU  C
   A  75  GLU  CB          2.51    -1.86     4.37  2.00e-01  4.77e+02  21.8*sigma
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51    -1.36     3.87  2.00e-01  3.74e+02  19.3*sigma

  Min. delta:    0.000
  Max. delta:    4.655
  Mean delta:    0.573

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.078       0.135      122.95   6.7*sigma

  Min. delta:    0.000
  Max. delta:    0.087
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   140.87   -19.17  1.80e+00  1.13e+02  10.7*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   118.31    12.89  1.30e+00  9.83e+01   9.9*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   128.30   -18.20  1.90e+00  9.18e+01   9.6*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   136.43   -14.73  1.80e+00  6.69e+01   8.2*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   122.57   -12.07  1.50e+00  6.47e+01   8.0*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   135.40   -13.70  1.80e+00  5.80e+01   7.6*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   126.10   -14.50  2.00e+00  5.26e+01   7.2*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG2       110.50   122.28   -11.78  1.70e+00  4.80e+01   6.9*sigma
   A 117  PRO  C
   A 117  PRO  CA
   A 117  PRO  CB        110.10   123.18   -13.08  1.90e+00  4.74e+01   6.9*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG1       110.40   121.10   -10.70  1.70e+00  3.96e+01   6.3*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  ND1       122.70   131.48    -8.78  1.50e+00  3.42e+01   5.9*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   131.99   -10.29  1.80e+00  3.27e+01   5.7*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   125.38    -8.48  1.50e+00  3.20e+01   5.7*sigma
   A  70  LEU  N
   A  70  LEU  CA
   A  70  LEU  CB        110.50   101.10     9.40  1.70e+00  3.06e+01   5.5*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   105.14    11.06  2.00e+00  3.06e+01   5.5*sigma
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   131.63    -9.93  1.80e+00  3.04e+01   5.5*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   123.76    -9.86  1.80e+00  3.00e+01   5.5*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00   126.02   -15.02  2.80e+00  2.88e+01   5.4*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   100.24     9.86  1.90e+00  2.69e+01   5.2*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   119.32    -8.82  1.70e+00  2.69e+01   5.2*sigma
   A 134  HIS  C
   A 134  HIS  CA
   A 134  HIS  CB        110.10   119.93    -9.83  1.90e+00  2.67e+01   5.2*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.64    -5.04  1.00e+00  2.54e+01   5.0*sigma
   A  70  LEU  C
   A  70  LEU  CA
   A  70  LEU  CB        110.10   119.46    -9.36  1.90e+00  2.43e+01   4.9*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   118.70    -8.30  1.70e+00  2.39e+01   4.9*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   100.86     9.24  1.90e+00  2.36e+01   4.9*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.30    -4.70  1.00e+00  2.21e+01   4.7*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   117.21    -4.61  1.00e+00  2.13e+01   4.6*sigma
   A 116  ASP  N
   A 116  ASP  CA
   A 116  ASP  CB        110.50   118.24    -7.74  1.70e+00  2.07e+01   4.6*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.30     5.90  1.30e+00  2.06e+01   4.5*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   129.80    -8.10  1.80e+00  2.03e+01   4.5*sigma
   A  71  ILE  C
   A  71  ILE  CA
   A  71  ILE  CB        111.60   102.74     8.86  2.00e+00  1.96e+01   4.4*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.03    -4.43  1.00e+00  1.96e+01   4.4*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   107.52     8.68  2.00e+00  1.88e+01   4.3*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  CB        110.50   117.87    -7.37  1.70e+00  1.88e+01   4.3*sigma
   A 118  ASP  C
   A 119  LEU     A  99  LEU  HA , Angle C-CA-HA, observed: 91.696, delta from target: 17.304

============================ Molprobity validation ============================

N
   A 119  LEU  CA        121.70   129.46    -7.76  1.80e+00  1.86e+01   4.3*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   113.97     7.73  1.80e+00  1.84e+01   4.3*sigma
   A  69  ALA  C
   A  70  LEU  N
   A  70  LEU  CA        121.70   129.41    -7.71  1.80e+00  1.84e+01   4.3*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   114.11     7.59  1.80e+00  1.78e+01   4.2*sigma
   A 135  HIS  N
   A 135  HIS  CA
   A 135  HIS  CB        110.50   117.63    -7.13  1.70e+00  1.76e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  CB        110.50   117.43    -6.93  1.70e+00  1.66e+01   4.1*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00   122.38   -11.38  2.80e+00  1.65e+01   4.1*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   122.37   -11.37  2.80e+00  1.65e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   19.174 (Z= 10.652)
  Mean delta:    2.806 (Z=  1.532)

                      ----------Dihedral angles----------                      


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.038   2242  Z= 0.491
    Angle     :  1.868  17.304   4079  Z= 0.820
    Chirality :  0.573   4.655    176
    Planarity :  0.012   0.075    327
    Dihedral  : 14.994  90.967    769
    Min Nonbonded Distance : 1.757
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  5.11 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  3.23 %
      Favored  : 91.94 %
    Cbeta Deviations :  3.03 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 1.53 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.93 (0.62), residues: 137
    helix: -0.41 (0.57), residues: 59
    sheet:  None (None), residues: 0
    loop : -2.06 (0.63), residues: 78
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.007   HIS A 139 
   PHE   0.074   0.013   PHE A  45 
   TYR   0.166   0.028   TYR A  50 
   ARG   0.072   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.007   HIS A 139 
   PHE   0.049   0.013   PHE A  45 
   TYR   0.135   0.031   TYR A  50 
   ARG   0.010   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   -94.07   -85.93  5.00e+00  2.95e+02  17.2*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   103.09    76.91  5.00e+00  2.37e+02  15.4*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -118.49   -61.51  5.00e+00  1.51e+02  12.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -118.55   -61.45  5.00e+00  1.51e+02  12.3*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00  -132.41   -47.59  5.00e+00  9.06e+01   9.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -133.23   -46.77  5.00e+00  8.75e+01   9.4*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   138.40    41.60  5.00e+00  6.92e+01   8.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   139.03    40.97  5.00e+00  6.71e+01   8.2*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   139.84    40.16  5.00e+00  6.45e+01   8.0*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   140.01    39.99  5.00e+00  6.40e+01   8.0*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   141.22    38.78  5.00e+00  6.02e+01   7.8*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -145.30   -34.70  5.00e+00  4.82e+01   6.9*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   145.71    34.29  5.00e+00  4.70e+01   6.9*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00  -147.08   -32.92  5.00e+00  4.34e+01   6.6*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   149.25    30.75  5.00e+00  3.78e+01   6.1*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   150.51    29.49  5.00e+00  3.48e+01   5.9*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -151.99   -28.01  5.00e+00  3.14e+01   5.6*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -152.13   -27.87  5.00e+00  3.11e+01   5.6*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00  -152.40   -27.60  5.00e+00  3.05e+01   5.5*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   153.46    26.54  5.00e+00  2.82e+01   5.3*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00  -156.75   -23.25  5.00e+00  2.16e+01   4.6*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   156.86    23.14  5.00e+00  2.14e+01   4.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00  -159.31   -20.69  5.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.001
  Max. delta:   85.931
  Mean delta:   17.004

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.85     5.36  2.00e-01  7.19e+02  26.8*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.66     5.30  2.00e-01  7.03e+02  26.5*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.34     4.98  2.00e-01  6.20e+02  24.9*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.20     4.71  2.00e-01  5.55e+02  23.6*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.15     4.66  2.00e-01  5.43e+02  23.3*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -1.76     4.20  2.00e-01  4.41e+02  21.0*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.12     3.55  2.00e-01  3.15e+02  17.8*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48     1.02     1.46  2.00e-01  5.36e+01   7.3*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51     1.67     0.84  2.00e-01  1.75e+01   4.2*sigma

  Min. delta:    0.000
  Max. delta:    5.362
  Mean delta:    0.967

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.141       0.111      398.76   5.5*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.066       0.107       85.94   5.4*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  ND1
   A 135  HIS  CD2
   A 135  HIS  CE1
   A 135  HIS  NE2           0.078       0.104       91.63   5.2*sigma
   A  76  SER  CA
   A  76  SER  C
   A  76  SER  O
   A  77  ILE  N             0.049       0.085       24.36   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.141
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  71  ILE  HB , Angle CA-CB-HB, observed: 95.994, delta from target: 13.006
   A 122  ILE  HB , Angle CA-CB-HB, observed: 95.958, delta from target: 13.042
   A 135  HIS  HA , Angle N-CA-HA, observed: 96.812, delta from target: 13.188
   A 124  ALA  HA , Angle CB-CA-HA, observed: 95.578, delta from target: 13.422
   A  79  LYS  HA , Angle N-CA-HA, observed: 96.138, delta from target: 13.862
   A 117  PRO  HA , Angle C-CA-HA, observed: 94.278, delta from target: 14.722
   A 127  ARG  HA , Angle C-CA-HA, observed: 91.617, delta from target: 17.383
   A 126  VAL  HA , Angle C-CA-HA, observed: 89.772, delta from target: 19.228
   A  51  ILE  HA , Angle CB-CA-HA, observed: 89.405, delta from target: 19.595
   A  51  ILE  HA , Angle C-CA-HA, observed: 88.587, delta from target: 20.413
   A 124  ALA  HA , Angle C-CA-HA, observed: 88.361, delta from target: 20.639
   A  74  ASP  HA , Angle C-CA-HA, observed: 86.564, delta from target: 22.436

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.093   2242  Z= 0.547
    Angle     :  2.541  22.436   4079  Z= 1.128
    Chirality :  0.967   5.362    176
    Planarity :  0.014   0.137    327
    Dihedral  : 14.325  85.931    769
    Min Nonbonded Distance : 1.639
  
  Molprobity Statistics.
    All-atom Clashscore : 14.88
    Ramachandran Plot:
      Outliers :  9.49 %
      Allowed  :  5.11 %
      Favored  : 85.40 %
    Rotamer:
      Outliers :  8.06 %
      Allowed  :  4.03 %
      Favored  : 87.90 %
    Cbeta Deviations : 13.64 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 10.69 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.71 (0.64), residues: 137
    helix: -1.41 (0.57), residues: 64
    sheet:  None (None), residues: 0
    loop : -2.18 (0.68), residues: 73
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A 135 
   PHE   0.017   0.006   PHE A  15 
   TYR   0.293   0.031   TYR A  91 
   ARG   0.025   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A 135 
   PHE   0.013   0.006   PHE A  45 
   TYR   0.242   0.036   TYR A  91 
   ARG   0.003   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   8.76 %
                favored =  78.83 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    18
  Clashscore            =  19.40
  RMS(bonds)            =   0.0135
  RMS(angles)           =   2.62
  MolProbity score      =   3.19

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.743)
  Mean delta:    0.013 (Z=  0.685)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 139  HIS  CA
   A 139  HIS  CB
   A 139  HIS  CG        113.80   124.10   -10.30  1.00e+00  1.06e+02  10.3*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   118.71    -4.91  1.00e+00  2.41e+01   4.9*sigma
   A 139  HIS  C
   A 139  HIS  CA
   A 139  HIS  CB        110.10   118.91    -8.81  1.90e+00  2.15e+01   4.6*sigma
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   129.97    -8.27  1.80e+00  2.11e+01   4.6*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.13     4.47  1.00e+00  1.99e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   116.69    -4.09  1.00e+00  1.67e+01   4.1*sigma
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        121.70   129.04    -7.34  1.80e+00  1.66e+01   4.1*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N         116.20   108.19     8.01  2.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.004 (Z=  0.001)
  Max. delta:   10.303 (Z= 10.303)
  Mean delta:    1.982 (Z=  1.112)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   150.64    29.36  5.00e+00  3.45e+01   5.9*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -153.62   -26.38  5.00e+00  2.78e+01   5.3*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   153.67    26.33  5.00e+00  2.77e+01   5.3*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   159.52    20.48  5.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.006
  Max. delta:   88.398
  Mean delta:   15.930

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  84  GLU  CA
   A  84  GLU  N
   A  84  GLU  C
   A  84  GLU  CB          2.51    -2.20     4.71  2.00e-01  5.55e+02  23.5*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -1.71     4.22  2.00e-01  4.46e+02  21.1*sigma
   A  83  THR  CA
   A  83  THR  N
   A  83  THR  C
   A  83  THR  CB          2.53     1.72     0.80  2.00e-01  1.61e+01   4.0*sigma

  Min. delta:    0.000
  Max. delta:    4.710
  Mean delta:    0.492

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.094       0.170      178.41   8.5*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  ND1
   A 139  HIS  CD2
   A 139  HIS  CE1
   A 139  HIS  NE2           0.067       0.113       67.51   5.7*sigma

  Min. delta:    0.000
  Max. delta:    0.094
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.039   2242  Z= 0.488
    Angle     :  1.806  10.721   4079  Z= 0.815
    Chirality :  0.492   4.710    176
    Planarity :  0.012   0.088    327
    Dihedral  : 13.211  88.398    769
    Min Nonbonded Distance : 1.783
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  5.84 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  0.81 %
      Favored  : 96.77 %
    Cbeta Deviations :  3.79 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.50 (0.66), residues: 137
    helix: -0.19 (0.62), residues: 59
    sheet:  None (None), residues: 0
    loop : -1.68 (0.67), residues: 78
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.017   0.005   HIS A 138 
   PHE   0.048   0.014   PHE A  45 
   TYR   0.208   0.017   TYR A  50 
   ARG   0.070   0.012   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.017   0.005   HIS A 138 
   PHE   0.037   0.015   PHE A  45 
   TYR   0.170   0.019   TYR A  50 
   ARG   0.009   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.67    -0.16  1.80e-02  7.75e+01   8.8*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.62    -0.17  1.90e-02  7.71e+01   8.8*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.62    -0.16  1.90e-02  6.92e+01   8.3*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     1.58    -0.12  1.90e-02  4.33e+01   6.6*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.42    -0.09  1.40e-02  4.27e+01   6.5*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.25     0.07  1.40e-02  2.82e+01   5.3*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.55    -0.10  1.90e-02  2.53e+01   5.0*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.55    -0.09  1.90e-02  2.47e+01   5.0*sigma
   A 124  ALA  C
   A 125  LYS  N           1.33     1.26     0.07  1.40e-02  2.41e+01   4.9*sigma
   A 129  ARG  N
   A 129  ARG  CA          1.46     1.54    -0.09  1.90e-02  2.05e+01   4.5*sigma
   A 131  ILE  CA
   A 131  ILE  C           1.52     1.61    -0.09  2.10e-02  1.83e+01   4.3*sigma
   A 126  VAL  CA
   A 126  VAL  C           1.52     1.44     0.09  2.10e-02  1.83e+01   4.3*sigma
   A 132  LEU  N
   A 132  LEU  CA          1.46     1.54    -0.08  1.90e-02  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.167 (Z=  8.803)
  Mean delta:    0.020 (Z=  1.043)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20    93.68    22.52  2.00e+00  1.27e+02  11.3*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   128.49   -17.99  1.70e+00  1.12e+02  10.6*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   124.78   -14.28  1.50e+00  9.06e+01   9.5*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   138.57   -16.87  1.80e+00  8.79e+01   9.4*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   125.92   -15.52  1.70e+00  8.33e+01   9.1*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   129.17   -17.57  2.00e+00  7.72e+01   8.8*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   136.04   -14.34  1.80e+00  6.35e+01   8.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.10   -11.20  1.50e+00  5.58e+01   7.5*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   122.91   -12.41  1.70e+00  5.33e+01   7.3*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   134.49   -12.79  1.80e+00  5.05e+01   7.1*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    99.61    11.89  1.70e+00  4.89e+01   7.0*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   130.42   -19.42  2.80e+00  4.81e+01   6.9*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   130.02   -13.82  2.00e+00  4.78e+01   6.9*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   122.15   -11.65  1.70e+00  4.70e+01   6.9*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40    98.42    12.98  1.90e+00  4.67e+01   6.8*sigma
   A 122  ILE  C
   A 122  ILE  CA
   A 122  ILE  CB        111.60   124.52   -12.92  2.00e+00  4.18e+01   6.5*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   121.30   -10.90  1.70e+00  4.11e+01   6.4*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   110.18    11.52  1.80e+00  4.09e+01   6.4*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10    98.06    12.04  1.90e+00  4.02e+01   6.3*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   100.77    10.73  1.70e+00  3.98e+01   6.3*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   125.21   -11.31  1.80e+00  3.95e+01   6.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   103.67    12.53  2.00e+00  3.92e+01   6.3*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   110.53    11.17  1.80e+00  3.85e+01   6.2*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.84   -11.14  1.80e+00  3.83e+01   6.2*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   132.50   -10.80  1.80e+00  3.60e+01   6.0*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.60    -6.00  1.00e+00  3.60e+01   6.0*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   125.70   -11.60  2.00e+00  3.36e+01   5.8*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40   102.16     8.24  1.50e+00  3.02e+01   5.5*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   131.51    -9.81  1.80e+00  2.97e+01   5.5*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   111.92     9.78  1.80e+00  2.95e+01   5.4*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N         116.20   105.35    10.85  2.00e+00  2.94e+01   5.4*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   131.45    -9.75  1.80e+00  2.93e+01   5.4*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   131.34    -9.64  1.80e+00  2.87e+01   5.4*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   131.26    -9.56  1.80e+00  2.82e+01   5.3*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   131.20    -9.50  1.80e+00  2.79e+01   5.3*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N         116.20   126.45   -10.25  2.00e+00  2.63e+01   5.1*sigma
   A 119  LEU  C
   A 119  LEU  CA
   A 119  LEU  CB        110.10   119.65    -9.55  1.90e+00  2.53e+01   5.0*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.60   -10.00  2.00e+00  2.50e+01   5.0*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   130.61    -8.91  1.80e+00  2.45e+01   4.9*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   118.92    -8.82  1.90e+00  2.15e+01   4.6*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG1       110.40   118.22    -7.82  1.70e+00  2.12e+01   4.6*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   115.82     7.18  1.60e+00  2.01e+01   4.5*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   117.08    -4.48  1.00e+00  2.01e+01   4.5*sigma
   A 122  ILE  O
   A 122  ILE  C
   A 123  GLU  N         123.00   115.84     7.16  1.60e+00  2.00e+01   4.5*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   118.00    -7.50  1.70e+00  1.95e+01   4.4*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  CB        110.50   103.05     7.45  1.70e+00  1.92e+01   4.4*sigma
   A 129  ARG  O
   A 129  ARG  C
   A 130  SER  N         123.00   129.97    -6.97  1.60e+00  1.90e+01   4.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   107.69     8.51  2.00e+00  1.81e+01   4.3*sigma
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        121.70   129.31    -7.61  1.80e+00  1.79e+01   4.2*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   117.67    -7.17  1.70e+00  1.78e+01   4.2*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  C         111.00   122.75   -11.75  2.80e+00  1.76e+01   4.2*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.80     5.40  1.30e+00  1.73e+01   4.2*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   103.46     7.04  1.70e+00  1.72e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   114.00     6.80  1.70e+00  1.60e+01   4.0*sigma

  Min. delta:    0.006 (Z=  0.001)
  Max. delta:   22.515 (Z= 11.258)
  Mean delta:    3.127 (Z=  1.675)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    71.22   108.78  5.00e+00  4.73e+02  21.8*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    72.61   107.39  5.00e+00  4.61e+02  21.5*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    96.32    83.68  5.00e+00  2.80e+02  16.7*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   101.09    78.91  5.00e+00  2.49e+02  15.8*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00  -103.30   -76.70  5.00e+00  2.35e+02  15.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   104.92    75.08  5.00e+00  2.25e+02  15.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -120.14   -59.86  5.00e+00  1.43e+02  12.0*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   120.70    59.30  5.00e+00  1.41e+02  11.9*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00  -121.54   -58.46  5.00e+00  1.37e+02  11.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -125.02   -54.98  5.00e+00  1.21e+02  11.0*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   129.30    50.70  5.00e+00  1.03e+02  10.1*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   134.87    45.13  5.00e+00  8.15e+01   9.0*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -135.63   -44.37  5.00e+00  7.87e+01   8.9*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -135.70   -44.30  5.00e+00  7.85e+01   8.9*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -138.93   -41.07  5.00e+00  6.75e+01   8.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA          0.00    38.21   -38.21  5.00e+00  5.84e+01   7.6*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   144.09    35.91  5.00e+00  5.16e+01   7.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -144.51   -35.49  5.00e+00  5.04e+01   7.1*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   145.55    34.45  5.00e+00  4.75e+01   6.9*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   145.76    34.24  5.00e+00  4.69e+01   6.8*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -148.02   -31.98  5.00e+00  4.09e+01   6.4*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   149.98    30.02  5.00e+00  3.61e+01   6.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   150.94    29.06  5.00e+00  3.38e+01   5.8*sigma
   A   1  MET  CA
   A   1  MET  C
   A   2  LEU  N
   A   2  LEU  CA        180.00   151.71    28.29  5.00e+00  3.20e+01   5.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   152.39    27.61  5.00e+00  3.05e+01   5.5*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -153.40   -26.60  5.00e+00  2.83e+01   5.3*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   154.22    25.78  5.00e+00  2.66e+01   5.2*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -157.03   -22.97  5.00e+00  2.11e+01   4.6*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   158.36    21.64  5.00e+00  1.87e+01   4.3*sigma
   A  38  ILE  CA
   A  38  ILE  C
   A  39  LEU  N
   A  39  LEU  CA        180.00   158.60    21.40  5.00e+00  1.83e+01   4.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -159.07   -20.93  5.00e+00  1.75e+01   4.2*sigma

  Min. delta:    0.022
  Max. delta:  108.775
  Mean delta:   20.273

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -3.04     5.55  2.00e-01  7.70e+02  27.7*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.79     5.30  2.00e-01  7.02e+02  26.5*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.52     5.16  2.00e-01  6.66e+02  25.8*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.51     5.15  2.00e-01  6.64e+02  25.8*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.37     5.01  2.00e-01  6.28e+02  25.1*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.43     4.95  2.00e-01  6.14e+02  24.8*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.43     4.86  2.00e-01  5.90e+02  24.3*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.25     4.80  2.00e-01  5.76e+02  24.0*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -2.29     4.80  2.00e-01  5.75e+02  24.0*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -2.27     4.76  2.00e-01  5.66e+02  23.8*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -1.11     3.54  2.00e-01  3.13e+02  17.7*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.09     3.52  2.00e-01  3.10e+02  17.6*sigma

  Min. delta:    0.000
  Max. delta:    5.549
  Mean delta:    1.269

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.053       0.092       56.39   4.6*sigma
   A  67  PHE  CB
   A  67  PHE  CG
   A  67  PHE  CD1
   A  67  PHE  CD2
   A  67  PHE  CE1
   A  67  PHE  CE2
   A  67  PHE  CZ            0.083       0.090      119.92   4.5*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O
   A 127  ARG  N             0.119       0.087      141.86   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.119
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 127  ARG  HA , Angle C-CA-HA, observed: 121.146, delta from target: -12.146
   A 124  ALA  HA , Angle C-CA-HA, observed: 95.668, delta from target: 13.332
   A 122  ILE  HA , Angle C-CA-HA, observed: 95.098, delta from target: 13.902
   A 119  LEU  HA , Angle CB-CA-HA, observed: 94.683, delta from target: 14.317
   A 126  VAL  HB , Angle CG1-CB-HB, observed: 93.499, delta from target: 14.501
   A  77  ILE  HA , Angle CB-CA-HA, observed: 94.467, delta from target: 14.533
   A 127  ARG  HA , Angle N-CA-HA, observed: 95.397, delta from target: 14.603
   A  78  ILE  HA , Angle N-CA-HA, observed: 95.037, delta from target: 14.963
   A  51  ILE  HA , Angle CB-CA-HA, observed: 93.735, delta from target: 15.265
   A 127  ARG  HA , Angle CB-CA-HA, observed: 93.236, delta from target: 15.764
   A  89  TYR  HA , Angle N-CA-HA, observed: 94.140, delta from target: 15.860
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.805, delta from target: 16.195
   A  91  TYR  HA , Angle CB-CA-HA, observed: 92.726, delta from target: 16.274
   A 126  VAL  HA , Angle CB-CA-HA, observed: 125.684, delta from target: -16.684
   A 131  ILE  HA , Angle C-CA-HA, observed: 92.009, delta from target: 16.991
   A  89  TYR  HA , Angle CB-CA-HA, observed: 128.491, delta from target: -19.491
   A  77  ILE  HB , Angle CA-CB-HB, observed: 85.548, delta from target: 23.452
   A  77  ILE  HA , Angle C-CA-HA, observed: 79.288, delta from target: 29.712

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.014   0.167   2242  Z= 0.742
    Angle     :  2.739  29.712   4079  Z= 1.218
    Chirality :  1.269   5.549    176
    Planarity :  0.015   0.119    327
    Dihedral  : 16.458 108.775    769
    Min Nonbonded Distance : 1.346
  
  Molprobity Statistics.
    All-atom Clashscore : 20.29
    Ramachandran Plot:
      Outliers : 13.14 %
      Allowed  :  6.57 %
      Favored  : 80.29 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  7.26 %
      Favored  : 85.48 %
    Cbeta Deviations :  9.85 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 16.03 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.36 (0.64), residues: 137
    helix: -1.87 (0.51), residues: 69
    sheet:  None (None), residues: 0
    loop : -2.62 (0.76), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A 137 
   PHE   0.196   0.033   PHE A  67 
   TYR   0.147   0.026   TYR A 105 
   ARG   0.039   0.009   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A 137 
   PHE   0.132   0.036   PHE A  67 
   TYR   0.121   0.031   TYR A  50 
   ARG   0.004   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  93.43 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     4
  Clashscore            =   0.90
  RMS(bonds)            =   0.0096
  RMS(angles)           =   1.87
  MolProbity score      =   1.72

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   9.49 %
                favored =  85.40 %
  Rotamer outliers      =   8.06 %
  C-beta deviations     =    18
  Clashscore            =  14.88
  RMS(bonds)            =   0.0106
  RMS(angles)           =   2.54
  MolProbity score      =   3.02

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  92.70 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     5
  Clashscore            =   1.80
  RMS(bonds)            =   0.0095
  RMS(angles)           =   1.81
  MolProbity score      =   1.69

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.054 (Z=  2.795)
  Mean delta:    0.013 (Z=  0.677)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   136.37   -22.47  1.80e+00  1.56e+02  12.5*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   126.55   -16.45  1.90e+00  7.50e+01   8.7*sigma
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   120.65    -8.05  1.00e+00  6.48e+01   8.0*sigma
   A 110  ASP  CA
   A 110  ASP  CB
   A 110  ASP  CG        112.60   117.72    -5.12  1.00e+00  2.63e+01   5.1*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   124.60     6.60  1.30e+00  2.58e+01   5.1*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  CB        110.50   102.48     8.02  1.70e+00  2.23e+01   4.7*sigma
   A 103  ASP  C
   A 103  ASP  CA
   A 103  ASP  CB        110.10   118.92    -8.82  1.90e+00  2.15e+01   4.6*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.39     4.21  1.00e+00  1.77e+01   4.2*sigma
   A  85  LYS  CA
   A  85  LYS  CB
   A  85  LYS  CG        114.10   122.52    -8.42  2.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   22.472 (Z= 12.484)
  Mean delta:    2.079 (Z=  1.149)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00    55.59   124.41  5.00e+00  6.19e+02  24.9*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -133.89   -46.11  5.00e+00  8.51e+01   9.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -147.16   -32.84  5.00e+00  4.31e+01   6.6*sigma
   A 101  LYS  CA
   A 101  LYS  C
   A 102  PRO  N
   A 102  PRO  CA        180.00   156.24    23.76  5.00e+00  2.26e+01   4.8*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00  -159.22   -20.78  5.00e+00  1.73e+01   4.2*sigma

  Min. delta:    0.011
  Max. delta:  124.409
  Mean delta:   17.964

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.24     4.75  2.00e-01  5.64e+02  23.7*sigma
   A  86  ILE  CA
   A  86  ILE  N
   A  86  ILE  C
   A  86  ILE  CB          2.43    -1.99     4.42  2.00e-01  4.89e+02  22.1*sigma

  Min. delta:    0.000
  Max. delta:    4.750
  Mean delta:    0.497

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.105       0.190      218.62   9.5*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.136       0.180      370.24   9.0*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  ND1
   A  43  HIS  CD2
   A  43  HIS  CE1
   A  43  HIS  NE2           0.097       0.132      140.54   6.6*sigma

  Min. delta:    0.000
  Max. delta:    0.136
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  89  TYR  HA , Angle C-CA-HA, observed: 93.011, delta from target: 15.989

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.054   2242  Z= 0.482
    Angle     :  1.866  22.472   4079  Z= 0.839
    Chirality :  0.497   4.750    176
    Planarity :  0.015   0.123    327
    Dihedral  : 15.204 124.409    769
    Min Nonbonded Distance : 1.666
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  8.76 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  6.45 %
      Favored  : 90.32 %
    Cbeta Deviations :  2.27 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.01 (0.69), residues: 137
    helix: -0.84 (0.54), residues: 66
    sheet:  None (None), residues: 0
    loop : -1.81 (0.82), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A  43 
   PHE   0.096   0.025   PHE A  67 
   TYR   0.260   0.039   TYR A  89 
   ARG   0.059   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A  43 
   PHE   0.053   0.022   PHE A  67 
   TYR   0.258   0.040   TYR A  89 
   ARG   0.006   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =  13.14 %
                favored =  80.29 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    13
  Clashscore            =  20.29
  RMS(bonds)            =   0.0140
  RMS(angles)           =   2.74
  MolProbity score      =   3.19

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.917, 37.618, 59.504, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   2.92 %
                favored =  88.32 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     3
  Clashscore            =   7.66
  RMS(bonds)            =   0.0094
  RMS(angles)           =   1.87
  MolProbity score      =   2.40

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.042 (Z=  2.707)
  Mean delta:    0.013 (Z=  0.647)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 112  VAL  CA
   A 112  VAL  CB
   A 112  VAL  CG1       110.40   125.22   -14.82  1.70e+00  7.60e+01   8.7*sigma
   A 107  LEU  C
   A 108  ILE  N
   A 108  ILE  CA        121.70   132.70   -11.00  1.80e+00  3.73e+01   6.1*sigma
   A 108  ILE  CB
   A 108  ILE  CG1
   A 108  ILE  CD1       113.80   126.03   -12.23  2.10e+00  3.39e+01   5.8*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   118.22    -5.62  1.00e+00  3.15e+01   5.6*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   124.60     6.60  1.30e+00  2.57e+01   5.1*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   117.30    -4.70  1.00e+00  2.21e+01   4.7*sigma
   A 112  VAL  CG1
   A 112  VAL  CB
   A 112  VAL  CG2       110.80   100.51    10.29  2.20e+00  2.19e+01   4.7*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.13     4.47  1.00e+00  2.00e+01   4.5*sigma
   A 111  TYR  C
   A 111  TYR  CA
   A 111  TYR  CB        110.10   118.43    -8.33  1.90e+00  1.92e+01   4.4*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   129.54    -7.84  1.80e+00  1.90e+01   4.4*sigma
   A  43  HIS  CA
   A  43  HIS  CB
   A  43  HIS  CG        113.80   118.02    -4.22  1.00e+00  1.78e+01   4.2*sigma
   A 136  HIS  ND1
   A 136  HIS  CG
   A 136  HIS  CD2       106.10   110.24    -4.14  1.00e+00  1.71e+01   4.1*sigma
   A  40  LYS  C
   A  40  LYS  CA
   A  40  LYS  CB        110.10   117.92    -7.82  1.90e+00  1.69e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.004 (Z=  0.002)
  Max. delta:   14.824 (Z=  8.720)
  Mean delta:    2.202 (Z=  1.221)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   148.67    31.33  5.00e+00  3.93e+01   6.3*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   154.06    25.94  5.00e+00  2.69e+01   5.2*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   158.76    21.24  5.00e+00  1.80e+01   4.2*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   159.61    20.39  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.072
  Max. delta:   84.858
  Mean delta:   15.457

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 108  ILE  CA
   A 108  ILE  N
   A 108  ILE  C
   A 108  ILE  CB          2.43    -1.78     4.22  2.00e-01  4.45e+02  21.1*sigma
   A 111  TYR  CA
   A 111  TYR  N
   A 111  TYR  C
   A 111  TYR  CB          2.51    -1.34     3.85  2.00e-01  3.71e+02  19.3*sigma

  Min. delta:    0.001
  Max. delta:    4.218
  Mean delta:    0.444

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.236       0.423     1110.28  21.2*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.169       0.297      571.42  14.9*sigma
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.076       0.113      100.82   5.7*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  ND1
   A 136  HIS  CD2
   A 136  HIS  CE1
   A 136  HIS  NE2           0.064       0.087       62.34   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.236
  Mean delta:    0.027

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 112  VAL  HB , Angle CA-CB-HB, observed: 96.872, delta from target: 12.128
   A 112  VAL  HB , Angle CG2-CB-HB, observed: 123.080, delta from target: -15.080
   A 111  TYR  HA , Angle C-CA-HA, observed: 91.698, delta from target: 17.302

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.042   2242  Z= 0.461
    Angle     :  1.969  17.302   4079  Z= 0.889
    Chirality :  0.444   4.218    176
    Planarity :  0.020   0.225    327
    Dihedral  : 13.238  84.858    769
    Min Nonbonded Distance : 1.627
  
  Molprobity Statistics.
    All-atom Clashscore : 9.47
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  : 10.22 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  6.45 %
      Favored  : 89.52 %
    Cbeta Deviations :  3.03 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.84 (0.76), residues: 137
    helix: -0.30 (0.66), residues: 54
    sheet:  None (None), residues: 0
    loop : -0.68 (0.81), residues: 83
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.029   0.010   HIS A  43 
   PHE   0.179   0.031   PHE A  15 
   TYR   0.530   0.054   TYR A 105 
   ARG   0.049   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.029   0.010   HIS A  43 
   PHE   0.113   0.031   PHE A  15 
   TYR   0.423   0.062   TYR A 105 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 137  HIS
   A 135  HIS
   A  66  GLN
   A 139  HIS

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.054)
  Mean delta:    0.013 (Z=  0.678)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A   1  MET  CA
   A   1  MET  C
   A   2  LEU  N         116.20   125.42    -9.22  2.00e+00  2.12e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.15     4.45  1.00e+00  1.98e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.62     5.58  1.30e+00  1.84e+01   4.3*sigma
   A   1  MET  O
   A   1  MET  C
   A   2  LEU  N         123.00   116.34     6.66  1.60e+00  1.73e+01   4.2*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   121.36    -7.46  1.80e+00  1.72e+01   4.1*sigma
   A  41  VAL  CG1
   A  41  VAL  CB
   A  41  VAL  CG2       110.80   101.83     8.97  2.20e+00  1.66e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.55     4.05  1.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    9.218 (Z=  4.609)
  Mean delta:    1.952 (Z=  1.059)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A   1  MET  CA
   A   1  MET  C
   A   2  LEU  N
   A   2  LEU  CA          0.00    39.95   -39.95  5.00e+00  6.38e+01   8.0*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   157.49    22.51  5.00e+00  2.03e+01   4.5*sigma

  Min. delta:    0.011
  Max. delta:   86.578
  Mean delta:   19.993

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.251
  Mean delta:    0.093

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.084       0.165      142.19   8.2*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.045       0.086       39.64   4.3*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  ND1
   A  43  HIS  CD2
   A  43  HIS  CE1
   A  43  HIS  NE2           0.061       0.082       55.34   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.092
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.483
    Angle     :  1.775   9.218   4079  Z= 0.783
    Chirality :  0.093   0.251    176
    Planarity :  0.014   0.080    327
    Dihedral  : 16.374  86.578    769
    Min Nonbonded Distance : 1.792
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  7.30 %
      Favored  : 92.70 %
    Rotamer:
      Outliers : 12.10 %
      Allowed  :  8.87 %
      Favored  : 79.03 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.33 (0.71), residues: 137
    helix: -0.47 (0.50), residues: 85
    sheet:  None (None), residues: 0
    loop : -1.42 (1.00), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A 135 
   PHE   0.124   0.022   PHE A  45 
   TYR   0.212   0.029   TYR A 111 
   ARG   0.077   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A 135 
   PHE   0.051   0.014   PHE A  45 
   TYR   0.165   0.031   TYR A 111 
   ARG   0.002   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.711)
  Mean delta:    0.013 (Z=  0.668)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   116.70     5.90  1.00e+00  3.48e+01   5.9*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  CB        110.50   101.61     8.89  1.70e+00  2.73e+01   5.2*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   109.36     4.44  1.00e+00  1.98e+01   4.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.28     4.32  1.00e+00  1.87e+01   4.3*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.61     5.59  1.30e+00  1.85e+01   4.3*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.31     4.29  1.00e+00  1.84e+01   4.3*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   116.74    -4.14  1.00e+00  1.71e+01   4.1*sigma
   A 109  LYS  CA
   A 109  LYS  CB
   A 109  LYS  CG        114.10   106.05     8.05  2.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.889 (Z=  5.900)
  Mean delta:    1.949 (Z=  1.083)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00   158.89    21.11  5.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.049
  Max. delta:   90.139
  Mean delta:   19.547

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.255
  Mean delta:    0.090

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  67  PHE  CB
   A  67  PHE  CG
   A  67  PHE  CD1
   A  67  PHE  CD2
   A  67  PHE  CE1
   A  67  PHE  CE2
   A  67  PHE  CZ            0.105       0.167      192.13   8.3*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  ND1
   A 138  HIS  CD2
   A 138  HIS  CE1
   A 138  HIS  NE2           0.081       0.110       99.51   5.5*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.065       0.103       83.86   5.2*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  ND1
   A 139  HIS  CD2
   A 139  HIS  CE1
   A 139  HIS  NE2           0.066       0.089       66.08   4.5*sigma

  Min. delta:    0.000
  Max. delta:    0.127
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.475
    Angle     :  1.754   8.889   4079  Z= 0.791
    Chirality :  0.090   0.255    176
    Planarity :  0.015   0.121    327
    Dihedral  : 16.097  90.139    769
    Min Nonbonded Distance : 1.711
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  8.03 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  6.45 %
      Favored  : 86.29 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.65 (0.66), residues: 137
    helix: -1.10 (0.50), residues: 56
    sheet:  None (None), residues: 0
    loop : -1.05 (0.74), residues: 81
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.005   HIS A 138 
   PHE   0.253   0.037   PHE A  67 
   TYR   0.204   0.031   TYR A  89 
   ARG   0.097   0.014   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.005   HIS A 138 
   PHE   0.167   0.038   PHE A  67 
   TYR   0.126   0.029   TYR A  12 
   ARG   0.006   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 138  HIS

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  89.78 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     4
  Clashscore            =   9.47
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.97
  MolProbity score      =   2.52

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.00 %
                favored =  92.70 %
  Rotamer outliers      =  12.10 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.78
  MolProbity score      =   2.54

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  91.24 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.75
  MolProbity score      =   2.32

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.64    -0.12  2.10e-02  3.23e+01   5.7*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.54    -0.09  1.60e-02  3.04e+01   5.5*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.55    -0.10  1.90e-02  2.53e+01   5.0*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.61    -0.09  2.10e-02  1.71e+01   4.1*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.39    -0.06  1.40e-02  1.68e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.119 (Z=  5.683)
  Mean delta:    0.015 (Z=  0.798)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   135.79   -14.09  1.80e+00  6.13e+01   7.8*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   135.62   -13.92  1.80e+00  5.98e+01   7.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   135.44   -13.74  1.80e+00  5.83e+01   7.6*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   124.45   -14.35  1.90e+00  5.70e+01   7.6*sigma
   A  93  LEU  O
   A  93  LEU  C
   A  94  GLY  N         123.00   111.08    11.92  1.60e+00  5.55e+01   7.5*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   127.08   -12.98  2.00e+00  4.21e+01   6.5*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  C         111.00    92.98    18.02  2.80e+00  4.14e+01   6.4*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   121.05   -10.55  1.70e+00  3.85e+01   6.2*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   132.46   -10.76  1.80e+00  3.57e+01   6.0*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50   101.90     9.60  1.70e+00  3.19e+01   5.6*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N         116.20   105.01    11.19  2.00e+00  3.13e+01   5.6*sigma
   A  83  THR  C
   A  83  THR  CA
   A  83  THR  CB        109.10   120.98   -11.88  2.20e+00  2.92e+01   5.4*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  C         111.00   125.75   -14.75  2.80e+00  2.77e+01   5.3*sigma
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG2       110.50   119.40    -8.90  1.70e+00  2.74e+01   5.2*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   104.93     7.07  1.40e+00  2.55e+01   5.0*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   112.62     9.08  1.80e+00  2.55e+01   5.0*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   119.00    -8.50  1.70e+00  2.50e+01   5.0*sigma
   A  15  PHE  CA
   A  15  PHE  CB
   A  15  PHE  CG        113.80   108.85     4.95  1.00e+00  2.45e+01   4.9*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.36    -9.76  2.00e+00  2.38e+01   4.9*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   118.61    -8.21  1.70e+00  2.33e+01   4.8*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    97.57    13.43  2.80e+00  2.30e+01   4.8*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   122.32   -11.02  2.30e+00  2.29e+01   4.8*sigma
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   130.31    -8.61  1.80e+00  2.29e+01   4.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.38    -4.78  1.00e+00  2.28e+01   4.8*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.34    -4.74  1.00e+00  2.25e+01   4.7*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   130.18    -8.48  1.80e+00  2.22e+01   4.7*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   129.91    -8.21  1.80e+00  2.08e+01   4.6*sigma
   A  86  ILE  N
   A  86  ILE  CA
   A  86  ILE  CB        111.50   104.03     7.47  1.70e+00  1.93e+01   4.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   107.57    -4.57  1.10e+00  1.73e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   124.31    -8.11  2.00e+00  1.65e+01   4.1*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 132  LEU  O         120.80   127.62    -6.82  1.70e+00  1.61e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   18.024 (Z=  7.828)
  Mean delta:    2.600 (Z=  1.389)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00    87.60    92.40  5.00e+00  3.42e+02  18.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00    94.95    85.05  5.00e+00  2.89e+02  17.0*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00    95.39    84.61  5.00e+00  2.86e+02  16.9*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -109.70   -70.30  5.00e+00  1.98e+02  14.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -113.95   -66.05  5.00e+00  1.75e+02  13.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   130.72    49.28  5.00e+00  9.72e+01   9.9*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   137.36    42.64  5.00e+00  7.27e+01   8.5*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   139.03    40.97  5.00e+00  6.71e+01   8.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   141.71    38.29  5.00e+00  5.87e+01   7.7*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -145.75   -34.25  5.00e+00  4.69e+01   6.9*sigma
   A  50  TYR  CA
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        180.00   150.10    29.90  5.00e+00  3.58e+01   6.0*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   151.72    28.28  5.00e+00  3.20e+01   5.7*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00  -154.66   -25.34  5.00e+00  2.57e+01   5.1*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -155.73   -24.27  5.00e+00  2.36e+01   4.9*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -156.89   -23.11  5.00e+00  2.14e+01   4.6*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   156.91    23.09  5.00e+00  2.13e+01   4.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   157.08    22.92  5.00e+00  2.10e+01   4.6*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -157.21   -22.79  5.00e+00  2.08e+01   4.6*sigma

  Min. delta:    0.003
  Max. delta:   92.399
  Mean delta:   17.743

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.85     5.38  2.00e-01  7.23e+02  26.9*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.59     5.10  2.00e-01  6.49e+02  25.5*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.40     4.91  2.00e-01  6.03e+02  24.6*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.32     4.83  2.00e-01  5.84e+02  24.2*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.90     4.33  2.00e-01  4.69e+02  21.7*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64     1.76     0.88  2.00e-01  1.95e+01   4.4*sigma
   A  83  THR  CA
   A  83  THR  N
   A  83  THR  C
   A  83  THR  CB          2.53     1.68     0.85  2.00e-01  1.81e+01   4.2*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     1.68     0.83  2.00e-01  1.72e+01   4.1*sigma

  Min. delta:    0.000
  Max. delta:    5.377
  Mean delta:    0.850

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.113       0.133      224.25   6.6*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.073       0.086      106.02   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.139
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  88  ASP  HA , Angle CB-CA-HA, observed: 121.335, delta from target: -12.335
   A  89  TYR  HA , Angle CB-CA-HA, observed: 94.003, delta from target: 14.997
   A  77  ILE  HB , Angle CG2-CB-HB, observed: 91.980, delta from target: 17.020
   A  83  THR  HA , Angle CB-CA-HA, observed: 91.539, delta from target: 17.461

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.119   2242  Z= 0.568
    Angle     :  2.296  18.024   4079  Z= 1.015
    Chirality :  0.850   5.377    176
    Planarity :  0.016   0.139    327
    Dihedral  : 14.649  92.399    769
    Min Nonbonded Distance : 1.643
  
  Molprobity Statistics.
    All-atom Clashscore : 10.37
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  :  9.49 %
      Favored  : 82.48 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  1.61 %
      Favored  : 91.94 %
    Cbeta Deviations :  9.85 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 6.87 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.55 (0.75), residues: 137
    helix: -1.66 (0.53), residues: 69
    sheet:  None (None), residues: 0
    loop : -1.64 (0.95), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.278   0.038   PHE A  15 
   TYR   0.187   0.021   TYR A  89 
   ARG   0.015   0.004   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.184   0.040   PHE A  15 
   TYR   0.143   0.023   TYR A  89 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (80.349, 39.297, 53.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 128  MET  N
   A 128  MET  CA          1.46     1.68    -0.22  1.90e-02  1.33e+02  11.5*sigma
   A 132  LEU  N
   A 132  LEU  CA          1.46     1.67    -0.21  1.90e-02  1.25e+02  11.2*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.67    -0.21  1.90e-02  1.20e+02  11.0*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.70    -0.18  1.80e-02  1.04e+02  10.2*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.65    -0.19  1.90e-02  9.80e+01   9.9*sigma
   A 131  ILE  CA
   A 131  ILE  C           1.52     1.68    -0.16  2.10e-02  5.70e+01   7.6*sigma
   A 131  ILE  N
   A 131  ILE  CA          1.46     1.60    -0.14  1.90e-02  5.49e+01   7.4*sigma
   A 131  ILE  C
   A 132  LEU  N           1.33     1.42    -0.09  1.40e-02  4.40e+01   6.6*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.42    -0.09  1.40e-02  4.36e+01   6.6*sigma
   A 133  GLU  N
   A 133  GLU  CA          1.46     1.58    -0.12  1.90e-02  4.05e+01   6.4*sigma
   A 132  LEU  CA
   A 132  LEU  C           1.52     1.65    -0.13  2.10e-02  3.56e+01   6.0*sigma
   A  79  LYS  CA
   A  79  LYS  CB          1.53     1.64    -0.11  2.00e-02  2.77e+01   5.3*sigma
   A 123  GLU  C
   A 124  ALA  N           1.33     1.26     0.07  1.40e-02  2.64e+01   5.1*sigma
   A 126  VAL  CA
   A 126  VAL  C           1.52     1.42     0.11  2.10e-02  2.54e+01   5.0*sigma
   A 130  SER  CA
   A 130  SER  C           1.52     1.63    -0.10  2.10e-02  2.37e+01   4.9*sigma
   A  78  ILE  N
   A  78  ILE  CA          1.46     1.54    -0.08  1.90e-02  1.71e+01   4.1*sigma
   A 134  HIS  N
   A 134  HIS  CA          1.46     1.54    -0.08  1.90e-02  1.66e+01   4.1*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.53    -0.08  1.90e-02  1.64e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.219 (Z= 11.513)
  Mean delta:    0.024 (Z=  1.244)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   143.36   -21.66  1.80e+00  1.45e+02  12.0*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    88.76    21.34  1.90e+00  1.26e+02  11.2*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20    96.22    19.98  2.00e+00  9.98e+01  10.0*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   128.50   -18.40  1.90e+00  9.37e+01   9.7*sigma
   A  39  LEU  C
   A  39  LEU  CA
   A  39  LEU  CB        110.10   128.27   -18.17  1.90e+00  9.15e+01   9.6*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   138.54   -16.84  1.80e+00  8.75e+01   9.4*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   127.50   -17.40  1.90e+00  8.38e+01   9.2*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    96.01    15.49  1.70e+00  8.30e+01   9.1*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   137.44   -15.74  1.80e+00  7.65e+01   8.7*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   137.04   -15.34  1.80e+00  7.26e+01   8.5*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50    98.33    13.17  1.70e+00  6.00e+01   7.7*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   123.35   -12.85  1.70e+00  5.71e+01   7.6*sigma
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        121.70   135.07   -13.37  1.80e+00  5.51e+01   7.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   126.43   -14.83  2.00e+00  5.50e+01   7.4*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   134.77   -13.07  1.80e+00  5.27e+01   7.3*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   134.73   -13.03  1.80e+00  5.24e+01   7.2*sigma
   A 132  LEU  N
   A 132  LEU  CA
   A 132  LEU  C         111.00   131.20   -20.20  2.80e+00  5.21e+01   7.2*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   134.58   -12.88  1.80e+00  5.12e+01   7.2*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   123.08   -12.98  1.90e+00  4.66e+01   6.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   102.59    13.61  2.00e+00  4.63e+01   6.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   132.25   -11.45  1.70e+00  4.54e+01   6.7*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   127.07   -12.97  2.00e+00  4.21e+01   6.5*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N         116.20   129.04   -12.84  2.00e+00  4.12e+01   6.4*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   133.13   -11.43  1.80e+00  4.03e+01   6.3*sigma
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        121.70   110.92    10.78  1.80e+00  3.59e+01   6.0*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.57    -5.97  1.00e+00  3.56e+01   6.0*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   132.43   -10.73  1.80e+00  3.56e+01   6.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   128.10   -11.90  2.00e+00  3.54e+01   5.9*sigma
   A 132  LEU  C
   A 132  LEU  CA
   A 132  LEU  CB        110.10    98.84    11.26  1.90e+00  3.52e+01   5.9*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   111.27    10.43  1.80e+00  3.36e+01   5.8*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   125.58    -8.68  1.50e+00  3.35e+01   5.8*sigma
   A 133  GLU  N
   A 133  GLU  CA
   A 133  GLU  C         111.00   126.65   -15.65  2.80e+00  3.13e+01   5.6*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   102.07     9.43  1.70e+00  3.08e+01   5.5*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   131.61    -9.91  1.80e+00  3.03e+01   5.5*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   120.53   -10.43  1.90e+00  3.01e+01   5.5*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.16    -9.46  1.80e+00  2.76e+01   5.3*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   121.82   -10.22  2.00e+00  2.61e+01   5.1*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   119.03    -8.63  1.70e+00  2.58e+01   5.1*sigma
   A  39  LEU  CA
   A  39  LEU  C
   A  40  LYS  N         116.20   126.33   -10.13  2.00e+00  2.57e+01   5.1*sigma
   A 103  ASP  C
   A 103  ASP  CA
   A 103  ASP  CB        110.10   100.84     9.26  1.90e+00  2.38e+01   4.9*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   130.35    -8.65  1.80e+00  2.31e+01   4.8*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   106.61     9.59  2.00e+00  2.30e+01   4.8*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   118.63    -8.13  1.70e+00  2.29e+01   4.8*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   106.66     9.54  2.00e+00  2.28e+01   4.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N         116.20   106.78     9.42  2.00e+00  2.22e+01   4.7*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  CB        110.50   102.62     7.88  1.70e+00  2.15e+01   4.6*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N         116.20   106.96     9.24  2.00e+00  2.14e+01   4.6*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   120.09    -8.69  1.90e+00  2.09e+01   4.6*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.74    -6.34  1.40e+00  2.05e+01   4.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O         120.80   128.41    -7.61  1.70e+00  2.00e+01   4.5*sigma
   A 103  ASP  N
   A 103  ASP  CA
   A 103  ASP  CB        110.50   118.01    -7.51  1.70e+00  1.95e+01   4.4*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   115.94     7.06  1.60e+00  1.95e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.50     5.70  1.30e+00  1.92e+01   4.4*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  C         111.00    98.75    12.25  2.80e+00  1.91e+01   4.4*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  C         111.00   123.10   -12.10  2.80e+00  1.87e+01   4.3*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  CD2       131.20   125.61     5.59  1.30e+00  1.85e+01   4.3*sigma
   A 102  PRO  C
   A 103  ASP  N
   A 103  ASP  CA        121.70   129.32    -7.62  1.80e+00  1.79e+01   4.2*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.75e+01   4.2*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   129.22    -7.52  1.80e+00  1.74e+01   4.2*sigma
   A 126  VAL  O
   A 126  VAL  C
   A 127  ARG  N         123.00   129.63    -6.63  1.60e+00  1.71e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.70e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma
   A 103  ASP  N
   A 103  ASP  CA
   A 103  ASP  C         111.00    99.58    11.42  2.80e+00  1.66e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   21.658 (Z= 12.032)
  Mean delta:    3.312 (Z=  1.770)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    62.39   117.61  5.00e+00  5.53e+02  23.5*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    75.20   104.80  5.00e+00  4.39e+02  21.0*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   -77.47  -102.53  5.00e+00  4.21e+02  20.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -80.30   -99.70  5.00e+00  3.98e+02  19.9*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   -86.98   -93.02  5.00e+00  3.46e+02  18.6*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -107.82   -72.18  5.00e+00  2.08e+02  14.4*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   108.04    71.96  5.00e+00  2.07e+02  14.4*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00  -115.65   -64.35  5.00e+00  1.66e+02  12.9*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   123.37    56.63  5.00e+00  1.28e+02  11.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   123.46    56.54  5.00e+00  1.28e+02  11.3*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00   130.80    49.20  5.00e+00  9.68e+01   9.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -132.82   -47.18  5.00e+00  8.90e+01   9.4*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   132.88    47.12  5.00e+00  8.88e+01   9.4*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -135.75   -44.25  5.00e+00  7.83e+01   8.8*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   140.70    39.30  5.00e+00  6.18e+01   7.9*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -147.04   -32.96  5.00e+00  4.35e+01   6.6*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   148.84    31.16  5.00e+00  3.88e+01   6.2*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   149.44    30.56  5.00e+00  3.73e+01   6.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -151.93   -28.07  5.00e+00  3.15e+01   5.6*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -152.17   -27.83  5.00e+00  3.10e+01   5.6*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -152.37   -27.63  5.00e+00  3.05e+01   5.5*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   154.32    25.68  5.00e+00  2.64e+01   5.1*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -154.36   -25.64  5.00e+00  2.63e+01   5.1*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   155.26    24.74  5.00e+00  2.45e+01   4.9*sigma
   A  38  ILE  CA
   A  38  ILE  C
   A  39  LEU  N
   A  39  LEU  CA        180.00   156.02    23.98  5.00e+00  2.30e+01   4.8*sigma

  Min. delta:    0.079
  Max. delta:  117.613
  Mean delta:   20.970

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -3.15     5.66  2.00e-01  8.01e+02  28.3*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.13     5.64  2.00e-01  7.96e+02  28.2*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.61     5.25  2.00e-01  6.89e+02  26.3*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -2.49     5.00  2.00e-01  6.25e+02  25.0*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.10     4.74  2.00e-01  5.63e+02  23.7*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.12     4.63  2.00e-01  5.35e+02  23.1*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -2.10     4.61  2.00e-01  5.30e+02  23.0*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -1.93     4.44  2.00e-01  4.92e+02  22.2*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.93     4.36  2.00e-01  4.75e+02  21.8*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.12     3.55  2.00e-01  3.16e+02  17.8*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.67     0.84  2.00e-01  1.77e+01   4.2*sigma

  Min. delta:    0.000
  Max. delta:    5.661
  Mean delta:    1.166

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O
   A 126  VAL  N             0.064       0.111       41.09   5.5*sigma
   A 128  MET  CA
   A 128  MET  C
   A 128  MET  O
   A 129  ARG  N             0.058       0.101       33.85   5.0*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.049       0.085       48.53   4.2*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O
   A  78  ILE  N             0.048       0.083       22.93   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.078
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 124  ALA  HA , Angle C-CA-HA, observed: 96.746, delta from target: 12.254
   A 123  GLU  HA , Angle N-CA-HA, observed: 122.451, delta from target: -12.451
   A  39  LEU  HA , Angle N-CA-HA, observed: 122.592, delta from target: -12.592
   A  89  TYR  HA , Angle CB-CA-HA, observed: 95.912, delta from target: 13.088
   A 129  ARG  HA , Angle C-CA-HA, observed: 95.712, delta from target: 13.288
   A  39  LEU  HA , Angle CB-CA-HA, observed: 95.652, delta from target: 13.348
   A  74  ASP  HA , Angle C-CA-HA, observed: 95.298, delta from target: 13.702
   A 103  ASP  HA , Angle C-CA-HA, observed: 123.703, delta from target: -14.703
   A  79  LYS  HA , Angle C-CA-HA, observed: 124.447, delta from target: -15.447
   A 133  GLU  HA , Angle N-CA-HA, observed: 92.901, delta from target: 17.099
   A 132  LEU  HA , Angle CB-CA-HA, observed: 126.915, delta from target: -17.915
   A 131  ILE  HA , Angle C-CA-HA, observed: 90.384, delta from target: 18.616
   A  51  ILE  HA , Angle CB-CA-HA, observed: 89.421, delta from target: 19.579
   A  51  ILE  HA , Angle C-CA-HA, observed: 87.980, delta from target: 21.020
   A 132  LEU  HA , Angle N-CA-HA, observed: 88.515, delta from target: 21.485
   A 127  ARG  HA , Angle CB-CA-HA, observed: 84.723, delta from target: 24.277
   A 123  GLU  HA , Angle CB-CA-HA, observed: 84.479, delta from target: 24.521

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.017   0.219   2242  Z= 0.886
    Angle     :  2.854  24.521   4079  Z= 1.276
    Chirality :  1.166   5.661    176
    Planarity :  0.014   0.072    327
    Dihedral  : 16.937 117.613    769
    Min Nonbonded Distance : 1.527
  
  Molprobity Statistics.
    All-atom Clashscore : 19.84
    Ramachandran Plot:
      Outliers :  8.76 %
      Allowed  : 13.14 %
      Favored  : 78.10 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  5.65 %
      Favored  : 87.90 %
    Cbeta Deviations : 15.15 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 13.74 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.36 (0.66), residues: 137
    helix: -2.56 (0.49), residues: 63
    sheet:  None (None), residues: 0
    loop : -1.88 (0.78), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.003   HIS A  43 
   PHE   0.076   0.017   PHE A  67 
   TYR   0.181   0.025   TYR A  50 
   ARG   0.051   0.009   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.003   HIS A  43 
   PHE   0.053   0.019   PHE A  67 
   TYR   0.147   0.026   TYR A  50 
   ARG   0.002   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Ramachandran outliers =   8.03 %
                favored =  82.48 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    13
  Clashscore            =  10.37
  RMS(bonds)            =   0.0109
  RMS(angles)           =   2.30
  MolProbity score      =   2.85

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.032 (Z=  1.543)
  Mean delta:    0.001 (Z=  0.063)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.599 (Z=  1.373)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   80.492
  Mean delta:   23.777

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.095
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.032   2241  Z= 0.046
    Angle     :  0.980   4.820   4077  Z= 0.342
    Chirality :  0.035   0.095    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.321  80.492    768
    Min Nonbonded Distance : 1.459
  
  Molprobity Statistics.
    All-atom Clashscore : 18.49
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  : 18.25 %
      Favored  : 77.37 %
    Rotamer:
      Outliers : 27.42 %
      Allowed  : 22.58 %
      Favored  : 50.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.81 (0.44), residues: 137
    helix: -3.87 (0.43), residues: 66
    sheet:  None (None), residues: 0
    loop : -5.40 (0.42), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A  43 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.003   0.001   TYR A 111 
   ARG   0.001   0.000   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A  43 
   PHE   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   TYR A  12 
   ARG   0.001   0.000   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2200
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2200
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.048 (Z=  2.621)
  Mean delta:    0.014 (Z=  0.701)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  N
   A  83  THR  CA
   A  83  THR  CB        111.50   100.98    10.52  1.70e+00  3.83e+01   6.2*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   132.50   -10.80  1.80e+00  3.60e+01   6.0*sigma
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        121.70   132.30   -10.60  1.80e+00  3.47e+01   5.9*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   119.01    -8.61  1.70e+00  2.57e+01   5.1*sigma
   A  72  ASN  OD1
   A  72  ASN  CG
   A  72  ASN  ND2       122.60   117.91     4.69  1.00e+00  2.20e+01   4.7*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.92     4.68  1.00e+00  2.19e+01   4.7*sigma
   A  85  LYS  C
   A  85  LYS  CA
   A  85  LYS  CB        110.10   118.95    -8.85  1.90e+00  2.17e+01   4.7*sigma
   A 108  ILE  C
   A 109  LYS  N
   A 109  LYS  CA        121.70   130.05    -8.35  1.80e+00  2.15e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.08     4.52  1.00e+00  2.05e+01   4.5*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   117.01    -4.41  1.00e+00  1.95e+01   4.4*sigma
   A 136  HIS  CA
   A 136  HIS  CB
   A 136  HIS  CG        113.80   118.20    -4.40  1.00e+00  1.94e+01   4.4*sigma
   A  72  ASN  C
   A  72  ASN  CA
   A  72  ASN  CB        110.10   118.03    -7.93  1.90e+00  1.74e+01   4.2*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.83     5.37  1.30e+00  1.71e+01   4.1*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  74  ASP  O         120.80   127.82    -7.02  1.70e+00  1.71e+01   4.1*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   103.69     6.81  1.70e+00  1.60e+01   4.0*sigma

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:   10.798 (Z=  6.189)
  Mean delta:    2.343 (Z=  1.270)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   -71.94  -108.06  5.00e+00  4.67e+02  21.6*sigma
   A  71  ILE  CA
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        180.00  -129.02   -50.98  5.00e+00  1.04e+02  10.2*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -131.08   -48.92  5.00e+00  9.57e+01   9.8*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   147.38    32.62  5.00e+00  4.26e+01   6.5*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   150.79    29.21  5.00e+00  3.41e+01   5.8*sigma
   A 102  PRO  CA
   A 102  PRO  C
   A 103  ASP  N
   A 103  ASP  CA        180.00  -153.30   -26.70  5.00e+00  2.85e+01   5.3*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   155.78    24.22  5.00e+00  2.35e+01   4.8*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   156.10    23.90  5.00e+00  2.28e+01   4.8*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00  -157.57   -22.43  5.00e+00  2.01e+01   4.5*sigma
   A  89  TYR  CD1
   A  89  TYR  CE1
   A  89  TYR  CZ
   A  89  TYR  OH        180.00   159.77    20.23  5.00e+00  1.64e+01   4.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00  -159.86   -20.14  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001
  Max. delta:  108.057
  Mean delta:   16.898

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  72  ASN  CA
   A  72  ASN  N
   A  72  ASN  C
   A  72  ASN  CB          2.51    -1.63     4.14  2.00e-01  4.28e+02  20.7*sigma
   A  85  LYS  CA
   A  85  LYS  N
   A  85  LYS  C
   A  85  LYS  CB          2.51    -1.59     4.10  2.00e-01  4.20e+02  20.5*sigma

  Min. delta:    0.000
  Max. delta:    4.140
  Mean delta:    0.454

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.368       0.334     2715.78  16.7*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.071       0.141      101.50   7.0*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.058       0.111       67.29   5.5*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  ND1
   A 136  HIS  CD2
   A 136  HIS  CE1
   A 136  HIS  NE2           0.076       0.110       86.77   5.5*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  88  ASP  O
   A  89  TYR  N             0.047       0.081       21.84   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.368
  Mean delta:    0.033

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  76  SER  HA , Angle N-CA-HA, observed: 96.568, delta from target: 13.432
   A  74  ASP  HA , Angle N-CA-HA, observed: 96.016, delta from target: 13.984
   A  72  ASN  HA , Angle C-CA-HA, observed: 93.222, delta from target: 15.778
   A  85  LYS  HA , Angle C-CA-HA, observed: 93.206, delta from target: 15.794

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.048   2242  Z= 0.499
    Angle     :  2.076  15.794   4079  Z= 0.926
    Chirality :  0.454   4.140    176
    Planarity :  0.025   0.362    327
    Dihedral  : 14.402 108.057    769
    Min Nonbonded Distance : 1.615
  
  Molprobity Statistics.
    All-atom Clashscore : 9.02
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  9.49 %
      Favored  : 87.59 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  6.45 %
      Favored  : 89.52 %
    Cbeta Deviations :  3.79 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 3.05 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.68 (0.67), residues: 137
    helix: -0.77 (0.50), residues: 62
    sheet:  None (None), residues: 0
    loop : -1.39 (0.78), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.033   0.006   HIS A 134 
   PHE   0.097   0.017   PHE A  67 
   TYR   0.878   0.063   TYR A  89 
   ARG   0.092   0.023   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.033   0.006   HIS A 134 
   PHE   0.066   0.016   PHE A  67 
   TYR   0.681   0.068   TYR A  89 
   ARG   0.017   0.004   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   8.76 %
                favored =  78.10 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    20
  Clashscore            =  19.84
  RMS(bonds)            =   0.0168
  RMS(angles)           =   2.85
  MolProbity score      =   3.17

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 123  GLU  N
   A 123  GLU  CA          1.46     1.33     0.13  1.90e-02  4.53e+01   6.7*sigma
   A  93  LEU  CB
   A  93  LEU  CG          1.53     1.61    -0.08  2.00e-02  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.128 (Z=  6.727)
  Mean delta:    0.016 (Z=  0.830)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  C         111.00   149.74   -38.74  2.80e+00  1.91e+02  13.8*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   132.21   -21.81  1.70e+00  1.65e+02  12.8*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00   140.96   -29.96  2.80e+00  1.14e+02  10.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   139.12   -17.42  1.80e+00  9.36e+01   9.7*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   127.77   -16.27  1.70e+00  9.16e+01   9.6*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   133.28   -21.98  2.30e+00  9.13e+01   9.6*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   138.55   -16.85  1.80e+00  8.76e+01   9.4*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50    95.68    15.82  1.70e+00  8.66e+01   9.3*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    85.20    25.80  2.80e+00  8.49e+01   9.2*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10    91.52    17.58  2.20e+00  6.39e+01   8.0*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   135.96   -14.26  1.80e+00  6.28e+01   7.9*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    95.43    14.67  1.90e+00  5.97e+01   7.7*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   124.61   -14.51  1.90e+00  5.83e+01   7.6*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   123.14   -12.64  1.70e+00  5.52e+01   7.4*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   127.16   -13.26  1.80e+00  5.42e+01   7.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   125.99   -14.39  2.00e+00  5.18e+01   7.2*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   122.67   -12.57  1.90e+00  4.38e+01   6.6*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   112.50    10.50  1.60e+00  4.30e+01   6.6*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00   129.05   -18.05  2.80e+00  4.16e+01   6.4*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    97.93    12.17  1.90e+00  4.10e+01   6.4*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50    99.63    10.87  1.70e+00  4.09e+01   6.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   103.44    12.76  2.00e+00  4.07e+01   6.4*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   132.97   -11.27  1.80e+00  3.92e+01   6.3*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.58    -5.98  1.00e+00  3.57e+01   6.0*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD2       110.70   128.60   -17.90  3.00e+00  3.56e+01   6.0*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   104.28    11.92  2.00e+00  3.55e+01   6.0*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   122.68   -11.28  1.90e+00  3.52e+01   5.9*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.26   -10.56  1.80e+00  3.44e+01   5.9*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  C         111.00    94.77    16.23  2.80e+00  3.36e+01   5.8*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   120.31    -9.81  1.70e+00  3.33e+01   5.8*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   132.06   -10.36  1.80e+00  3.31e+01   5.8*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00    95.52    15.48  2.80e+00  3.06e+01   5.5*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   122.53   -10.93  2.00e+00  2.99e+01   5.5*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   119.75    -9.25  1.70e+00  2.96e+01   5.4*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N         116.20   105.44    10.76  2.00e+00  2.90e+01   5.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   124.87    -7.97  1.50e+00  2.82e+01   5.3*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   124.32     6.88  1.30e+00  2.80e+01   5.3*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    96.69    14.31  2.80e+00  2.61e+01   5.1*sigma
   A  98  SER  C
   A  98  SER  CA
   A  98  SER  CB        110.10   119.50    -9.40  1.90e+00  2.45e+01   4.9*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  C         111.00   124.35   -13.35  2.80e+00  2.27e+01   4.8*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   118.56    -8.06  1.70e+00  2.25e+01   4.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   125.49    -9.29  2.00e+00  2.16e+01   4.6*sigma
   A  93  LEU  CD1
   A  93  LEU  CG
   A  93  LEU  CD2       110.80   100.62    10.18  2.20e+00  2.14e+01   4.6*sigma
   A 125  LYS  C
   A 125  LYS  CA
   A 125  LYS  CB        110.10   118.86    -8.76  1.90e+00  2.13e+01   4.6*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   103.75     7.75  1.70e+00  2.08e+01   4.6*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  CB        110.50   102.81     7.69  1.70e+00  2.05e+01   4.5*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   129.76    -8.06  1.80e+00  2.01e+01   4.5*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   121.85    -7.95  1.80e+00  1.95e+01   4.4*sigma
   A 104  VAL  C
   A 104  VAL  CA
   A 104  VAL  CB        111.40   103.05     8.35  1.90e+00  1.93e+01   4.4*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   122.79    -8.69  2.00e+00  1.89e+01   4.3*sigma
   A 134  HIS  CA
   A 134  HIS  CB
   A 134  HIS  CG        113.80   109.48     4.32  1.00e+00  1.87e+01   4.3*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   117.78    -7.28  1.70e+00  1.83e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.39     4.21  1.00e+00  1.77e+01   4.2*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   107.87     8.33  2.00e+00  1.74e+01   4.2*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   114.23     7.47  1.80e+00  1.72e+01   4.1*sigma
   A 122  ILE  O
   A 122  ILE  C
   A 123  GLU  N         123.00   129.60    -6.60  1.60e+00  1.70e+01   4.1*sigma
   A 137  HIS  CA
   A 137  HIS  CB
   A 137  HIS  CG        113.80   117.87    -4.07  1.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   38.735 (Z= 13.834)
  Mean delta:    3.487 (Z=  1.766)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -67.11  -112.89  5.00e+00  5.10e+02  22.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    68.33   111.67  5.00e+00  4.99e+02  22.3*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   -79.48  -100.52  5.00e+00  4.04e+02  20.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    93.71    86.29  5.00e+00  2.98e+02  17.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    99.88    80.12  5.00e+00  2.57e+02  16.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   115.96    64.04  5.00e+00  1.64e+02  12.8*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   125.28    54.72  5.00e+00  1.20e+02  10.9*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   137.27    42.73  5.00e+00  7.30e+01   8.5*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   139.49    40.51  5.00e+00  6.56e+01   8.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   139.73    40.27  5.00e+00  6.49e+01   8.1*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   141.00    39.00  5.00e+00  6.08e+01   7.8*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -143.75   -36.25  5.00e+00  5.26e+01   7.3*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -147.80   -32.20  5.00e+00  4.15e+01   6.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   149.34    30.66  5.00e+00  3.76e+01   6.1*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00  -150.72   -29.28  5.00e+00  3.43e+01   5.9*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -151.19   -28.81  5.00e+00  3.32e+01   5.8*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA          0.00    28.17   -28.17  5.00e+00  3.17e+01   5.6*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   153.00    27.00  5.00e+00  2.92e+01   5.4*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   156.08    23.92  5.00e+00  2.29e+01   4.8*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   156.22    23.78  5.00e+00  2.26e+01   4.8*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   159.46    20.54  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.038
  Max. delta:  112.895
  Mean delta:   20.455

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.19     5.70  2.00e-01  8.12e+02  28.5*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.48     5.13  2.00e-01  6.58e+02  25.6*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.40     5.05  2.00e-01  6.37e+02  25.2*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.54     5.05  2.00e-01  6.36e+02  25.2*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.19     4.74  2.00e-01  5.62e+02  23.7*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.22     4.73  2.00e-01  5.60e+02  23.7*sigma
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51    -2.17     4.69  2.00e-01  5.49e+02  23.4*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.18     4.62  2.00e-01  5.33e+02  23.1*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.95     4.38  2.00e-01  4.80e+02  21.9*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -1.51     4.02  2.00e-01  4.05e+02  20.1*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.69     3.12  2.00e-01  2.44e+02  15.6*sigma
   A 126  VAL  CB
   A 126  VAL  CA
   A 126  VAL  CG1
   A 126  VAL  CG2        -2.63    -1.13    -1.50  2.00e-01  5.65e+01   7.5*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51     1.05     1.46  2.00e-01  5.33e+01   7.3*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51     1.54     0.97  2.00e-01  2.34e+01   4.8*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51     1.69     0.82  2.00e-01  1.67e+01   4.1*sigma

  Min. delta:    0.000
  Max. delta:    5.701
  Mean delta:    1.204

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.060       0.117       73.01   5.9*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  93  LEU  O
   A  94  GLY  N             0.061       0.105       37.18   5.3*sigma
   A 128  MET  CA
   A 128  MET  C
   A 128  MET  O
   A 129  ARG  N             0.056       0.096       31.11   4.8*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.095       0.093      181.54   4.7*sigma

  Min. delta:    0.000
  Max. delta:    0.095
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  98  SER  HA , Angle C-CA-HA, observed: 96.935, delta from target: 12.065
   A 128  MET  HA , Angle N-CA-HA, observed: 97.616, delta from target: 12.384
   A  77  ILE  HB , Angle CA-CB-HB, observed: 96.437, delta from target: 12.563
   A 125  LYS  HA , Angle CB-CA-HA, observed: 96.251, delta from target: 12.749
   A  88  ASP  HA , Angle N-CA-HA, observed: 97.196, delta from target: 12.804
   A 128  MET  HA , Angle CB-CA-HA, observed: 121.865, delta from target: -12.865
   A  92  THR  HA , Angle N-CA-HA, observed: 96.544, delta from target: 13.456
   A  93  LEU  HG , Angle CD1-CG-HG, observed: 122.119, delta from target: -14.119
   A  97  SER  HA , Angle N-CA-HA, observed: 95.080, delta from target: 14.920
   A  93  LEU  HA , Angle C-CA-HA, observed: 92.782, delta from target: 16.218
   A 126  VAL  HB , Angle CG1-CB-HB, observed: 91.615, delta from target: 16.385
   A 126  VAL  HA , Angle C-CA-HA, observed: 125.795, delta from target: -16.795
   A  79  LYS  HA , Angle C-CA-HA, observed: 126.183, delta from target: -17.183
   A 123  GLU  HA , Angle N-CA-HA, observed: 127.826, delta from target: -17.826
   A 128  MET  HA , Angle C-CA-HA, observed: 90.224, delta from target: 19.776
   A 126  VAL  HB , Angle CG2-CB-HB, observed: 128.314, delta from target: -20.314
   A  93  LEU  HA , Angle N-CA-HA, observed: 87.943, delta from target: 22.057
   A  93  LEU  HG , Angle CB-CG-HG, observed: 85.359, delta from target: 23.641
   A  51  ILE  HA , Angle C-CA-HA, observed: 84.898, delta from target: 24.102
   A  91  TYR  HA , Angle CB-CA-HA, observed: 84.467, delta from target: 24.533
   A  51  ILE  HA , Angle CB-CA-HA, observed: 81.648, delta from target: 27.352
   A 126  VAL  HA , Angle CB-CA-HA, observed: 80.569, delta from target: 28.431
   A 126  VAL  HB , Angle CA-CB-HB, observed: 76.733, delta from target: 32.267
   A  92  THR  HA , Angle CB-CA-HA, observed: 143.117, delta from target: -34.117
   A  93  LEU  HA , Angle CB-CA-HA, observed: 148.507, delta from target: -39.507

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.128   2242  Z= 0.591
    Angle     :  3.161  39.507   4079  Z= 1.333
    Chirality :  1.204   5.701    176
    Planarity :  0.012   0.093    327
    Dihedral  : 16.423 112.895    769
    Min Nonbonded Distance : 1.404
  
  Molprobity Statistics.
    All-atom Clashscore : 25.70
    Ramachandran Plot:
      Outliers :  7.30 %
      Allowed  :  8.76 %
      Favored  : 83.94 %
    Rotamer:
      Outliers : 10.48 %
      Allowed  :  7.26 %
      Favored  : 82.26 %
    Cbeta Deviations : 15.91 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 1.53 %
      Twisted Proline : 0.00 %
      Twisted General : 10.69 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.24 (0.58), residues: 137
    helix: -1.76 (0.55), residues: 56
    sheet:  None (None), residues: 0
    loop : -2.55 (0.58), residues: 81
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.004   HIS A 134 
   PHE   0.048   0.017   PHE A  15 
   TYR   0.237   0.027   TYR A  91 
   ARG   0.047   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.004   HIS A 134 
   PHE   0.030   0.013   PHE A  67 
   TYR   0.184   0.031   TYR A  91 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 0.64, per 1000 atoms: 0.29
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.877, 57.375, 44.684, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   4.38 %
                favored =  77.37 %
  Rotamer outliers      =  27.42 %
  C-beta deviations     =     0
  Clashscore            =  18.49
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.63

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.92 %
                favored =  87.59 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     5
  Clashscore            =   9.02
  RMS(bonds)            =   0.0096
  RMS(angles)           =   2.08
  MolProbity score      =   2.55

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.61    -0.16  1.60e-02  1.03e+02  10.1*sigma
   A  89  TYR  C
   A  90  SER  N           1.33     1.42    -0.09  1.40e-02  4.35e+01   6.6*sigma
   A  90  SER  N
   A  90  SER  CA          1.46     1.58    -0.12  1.90e-02  4.02e+01   6.3*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.65    -0.13  2.10e-02  3.64e+01   6.0*sigma
   A  99  LEU  CA
   A  99  LEU  C           1.52     1.43     0.10  2.10e-02  2.17e+01   4.7*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.162 (Z= 10.135)
  Mean delta:    0.017 (Z=  0.920)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70    97.90    23.80  1.80e+00  1.75e+02  13.2*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD1       110.70   137.50   -26.80  3.00e+00  7.98e+01   8.9*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   125.09   -14.59  1.70e+00  7.36e+01   8.6*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  89  TYR  O         120.80   106.28    14.52  1.70e+00  7.30e+01   8.5*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   126.00   -15.90  1.90e+00  7.00e+01   8.4*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   128.73   -14.83  1.80e+00  6.79e+01   8.2*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   127.73   -13.83  1.80e+00  5.91e+01   7.7*sigma
   A  93  LEU  CD1
   A  93  LEU  CG
   A  93  LEU  CD2       110.80    94.48    16.32  2.20e+00  5.50e+01   7.4*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10    96.15    13.95  1.90e+00  5.39e+01   7.3*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   134.79   -13.09  1.80e+00  5.29e+01   7.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   130.63   -14.43  2.00e+00  5.20e+01   7.2*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10    96.43    13.67  1.90e+00  5.18e+01   7.2*sigma
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        121.70   134.32   -12.62  1.80e+00  4.92e+01   7.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.42   -10.52  1.50e+00  4.92e+01   7.0*sigma
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        121.70   134.32   -12.62  1.80e+00  4.92e+01   7.0*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.22   -12.52  1.80e+00  4.84e+01   7.0*sigma
   A  85  LYS  C
   A  85  LYS  CA
   A  85  LYS  CB        110.10   123.11   -13.01  1.90e+00  4.69e+01   6.8*sigma
   A 100  GLN  C
   A 100  GLN  CA
   A 100  GLN  CB        110.10   122.81   -12.71  1.90e+00  4.47e+01   6.7*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   119.22    -6.62  1.00e+00  4.38e+01   6.6*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   127.19   -13.09  2.00e+00  4.29e+01   6.5*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    92.79    18.21  2.80e+00  4.23e+01   6.5*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N         116.20   103.19    13.01  2.00e+00  4.23e+01   6.5*sigma
   A  99  LEU  O
   A  99  LEU  C
   A 100  GLN  N         123.00   133.32   -10.32  1.60e+00  4.16e+01   6.5*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   133.22   -11.52  1.80e+00  4.09e+01   6.4*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N         116.20   103.51    12.69  2.00e+00  4.02e+01   6.3*sigma
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        121.70   132.97   -11.27  1.80e+00  3.92e+01   6.3*sigma
   A  95  ASP  C
   A  95  ASP  CA
   A  95  ASP  CB        110.10   121.95   -11.85  1.90e+00  3.89e+01   6.2*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   118.82    -6.22  1.00e+00  3.87e+01   6.2*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   121.04   -10.54  1.70e+00  3.84e+01   6.2*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   132.52   -10.82  1.80e+00  3.61e+01   6.0*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   120.24    -9.84  1.70e+00  3.35e+01   5.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.34    -5.74  1.00e+00  3.30e+01   5.7*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   132.01   -10.31  1.80e+00  3.28e+01   5.7*sigma
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG2       110.50   120.19    -9.69  1.70e+00  3.25e+01   5.7*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   122.50   -10.90  2.00e+00  2.97e+01   5.4*sigma
   A  86  ILE  C
   A  86  ILE  CA
   A  86  ILE  CB        111.60   122.49   -10.89  2.00e+00  2.96e+01   5.4*sigma
   A  95  ASP  N
   A  95  ASP  CA
   A  95  ASP  C         111.00    96.11    14.89  2.80e+00  2.83e+01   5.3*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   122.35   -11.05  2.30e+00  2.31e+01   4.8*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N         116.20   125.79    -9.59  2.00e+00  2.30e+01   4.8*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   130.06    -8.36  1.80e+00  2.16e+01   4.6*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   123.51   -12.51  2.80e+00  2.00e+01   4.5*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  CD2       131.20   125.52     5.68  1.30e+00  1.91e+01   4.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   107.52     8.68  2.00e+00  1.88e+01   4.3*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   129.28    -7.58  1.80e+00  1.77e+01   4.2*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  CB        110.50   117.64    -7.14  1.70e+00  1.77e+01   4.2*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   115.86    -6.26  1.50e+00  1.74e+01   4.2*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   117.60    -7.10  1.70e+00  1.74e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A 138  HIS  O
   A 138  HIS  C
   A 139  HIS  N         123.00   116.38     6.62  1.60e+00  1.71e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.69e+01   4.1*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   117.49    -6.99  1.70e+00  1.69e+01   4.1*sigma
   A  99  LEU  CA
   A  99  LEU  CB
   A  99  LEU  CG        116.30   130.65   -14.35  3.50e+00  1.68e+01   4.1*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  C         111.00   122.39   -11.39  2.80e+00  1.65e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   26.804 (Z= 13.222)
  Mean delta:    3.244 (Z=  1.687)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   -52.16  -127.84  5.00e+00  6.54e+02  25.6*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00    56.20   123.80  5.00e+00  6.13e+02  24.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00    62.84   117.16  5.00e+00  5.49e+02  23.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    81.76    98.24  5.00e+00  3.86e+02  19.6*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00    90.08    89.92  5.00e+00  3.23e+02  18.0*sigma
   A  70  LEU  CA
   A  70  LEU  C
   A  71  ILE  N
   A  71  ILE  CA        180.00   121.97    58.03  5.00e+00  1.35e+02  11.6*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -127.58   -52.42  5.00e+00  1.10e+02  10.5*sigma
   A  71  ILE  CA
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        180.00  -129.97   -50.03  5.00e+00  1.00e+02  10.0*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00  -137.61   -42.39  5.00e+00  7.19e+01   8.5*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   139.33    40.67  5.00e+00  6.62e+01   8.1*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -139.59   -40.41  5.00e+00  6.53e+01   8.1*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   142.17    37.83  5.00e+00  5.72e+01   7.6*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   142.50    37.50  5.00e+00  5.63e+01   7.5*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -146.09   -33.91  5.00e+00  4.60e+01   6.8*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -146.20   -33.80  5.00e+00  4.57e+01   6.8*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   148.86    31.14  5.00e+00  3.88e+01   6.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   149.08    30.92  5.00e+00  3.82e+01   6.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   149.85    30.15  5.00e+00  3.64e+01   6.0*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -151.68   -28.32  5.00e+00  3.21e+01   5.7*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   153.63    26.37  5.00e+00  2.78e+01   5.3*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -154.00   -26.00  5.00e+00  2.70e+01   5.2*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   156.13    23.87  5.00e+00  2.28e+01   4.8*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   158.65    21.35  5.00e+00  1.82e+01   4.3*sigma
   A  38  ILE  CA
   A  38  ILE  C
   A  39  LEU  N
   A  39  LEU  CA        180.00   159.31    20.69  5.00e+00  1.71e+01   4.1*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -159.39   -20.61  5.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.101
  Max. delta:  127.843
  Mean delta:   20.532

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -3.01     5.52  2.00e-01  7.63e+02  27.6*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.68     5.19  2.00e-01  6.74e+02  26.0*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.51     5.02  2.00e-01  6.31e+02  25.1*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51    -2.50     5.01  2.00e-01  6.27e+02  25.0*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.47     4.98  2.00e-01  6.20e+02  24.9*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.22     4.86  2.00e-01  5.91e+02  24.3*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.22     4.77  2.00e-01  5.69e+02  23.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.67     4.11  2.00e-01  4.21e+02  20.5*sigma
   A 100  GLN  CA
   A 100  GLN  N
   A 100  GLN  C
   A 100  GLN  CB          2.51    -1.08     3.59  2.00e-01  3.22e+02  17.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.04     3.48  2.00e-01  3.02e+02  17.4*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     0.09     2.42  2.00e-01  1.46e+02  12.1*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     0.60     1.91  2.00e-01  9.15e+01   9.6*sigma

  Min. delta:    0.001
  Max. delta:    5.524
  Mean delta:    1.157

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.126       0.157      315.66   7.8*sigma
   A  68  TYR  CB
   A  68  TYR  CG
   A  68  TYR  CD1
   A  68  TYR  CD2
   A  68  TYR  CE1
   A  68  TYR  CE2
   A  68  TYR  CZ
   A  68  TYR  OH            0.054       0.102       58.08   5.1*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.048       0.083       45.17   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.126
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  90  SER  H  , Angle C-N-H, observed: 136.308, delta from target: -12.008
   A  78  ILE  HB , Angle CG2-CB-HB, observed: 96.873, delta from target: 12.127
   A  92  THR  HB , Angle CA-CB-HB, observed: 96.703, delta from target: 12.297
   A  90  SER  HA , Angle N-CA-HA, observed: 96.943, delta from target: 13.057
   A  97  SER  HA , Angle CB-CA-HA, observed: 122.370, delta from target: -13.370
   A  95  ASP  HA , Angle N-CA-HA, observed: 123.406, delta from target: -13.406
   A  90  SER  HA , Angle CB-CA-HA, observed: 122.698, delta from target: -13.698
   A  93  LEU  HA , Angle CB-CA-HA, observed: 94.330, delta from target: 14.670
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.654, delta from target: 15.346
   A  99  LEU  HA , Angle N-CA-HA, observed: 94.504, delta from target: 15.496
   A  78  ILE  HA , Angle N-CA-HA, observed: 92.059, delta from target: 17.941
   A  77  ILE  HA , Angle C-CA-HA, observed: 90.817, delta from target: 18.183
   A  93  LEU  HG , Angle CB-CG-HG, observed: 88.315, delta from target: 20.685
   A 100  GLN  HA , Angle C-CA-HA, observed: 83.103, delta from target: 25.897
   A  93  LEU  HG , Angle CD2-CG-HG, observed: 135.400, delta from target: -27.400
   A  81  TYR  HA , Angle N-CA-HA, observed: 66.330, delta from target: 43.670
   A  97  SER  HA , Angle N-CA-HA, observed: 37.419, delta from target: 72.581

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.162   2242  Z= 0.655
    Angle     :  3.089  72.581   4079  Z= 1.301
    Chirality :  1.157   5.524    176
    Planarity :  0.014   0.168    327
    Dihedral  : 16.349 127.843    769
    Min Nonbonded Distance : 1.399
  
  Molprobity Statistics.
    All-atom Clashscore : 25.70
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  : 14.60 %
      Favored  : 79.56 %
    Rotamer:
      Outliers : 12.90 %
      Allowed  :  1.61 %
      Favored  : 85.48 %
    Cbeta Deviations : 12.88 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 13.74 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.34 (0.61), residues: 137
    helix: -2.65 (0.44), residues: 82
    sheet:  None (None), residues: 0
    loop : -3.08 (0.85), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.004   HIS A  43 
   PHE   0.056   0.013   PHE A  67 
   TYR   0.305   0.035   TYR A  81 
   ARG   0.028   0.005   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.004   HIS A  43 
   PHE   0.038   0.013   PHE A  67 
   TYR   0.165   0.037   TYR A  81 
   ARG   0.004   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== Collecting inputs ==============================

  Ramachandran outliers =   7.30 %
                favored =  83.94 %
  Rotamer outliers      =  10.48 %
  C-beta deviations     =    21
  Clashscore            =  25.70
  RMS(bonds)            =   0.0114
  RMS(angles)           =   3.16
  MolProbity score      =   3.35

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 132  LEU  N
   A 132  LEU  CA          1.46     1.68    -0.22  1.90e-02  1.35e+02  11.6*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.67    -0.21  1.90e-02  1.19e+02  10.9*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     1.65    -0.19  1.90e-02  1.02e+02  10.1*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.69    -0.18  1.80e-02  9.55e+01   9.8*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.64    -0.18  1.90e-02  9.18e+01   9.6*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.43    -0.10  1.40e-02  4.84e+01   7.0*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.57    -0.11  1.90e-02  3.58e+01   6.0*sigma
   A 123  GLU  N
   A 123  GLU  CA          1.46     1.57    -0.11  1.90e-02  3.30e+01   5.7*sigma
   A 131  ILE  CA
   A 131  ILE  C           1.52     1.64    -0.11  2.10e-02  2.99e+01   5.5*sigma
   A 125  LYS  N
   A 125  LYS  CA          1.46     1.56    -0.10  1.90e-02  2.69e+01   5.2*sigma
   A 133  GLU  N
   A 133  GLU  CA          1.46     1.56    -0.10  1.90e-02  2.65e+01   5.1*sigma
   A 131  ILE  N
   A 131  ILE  CA          1.46     1.55    -0.09  1.90e-02  2.38e+01   4.9*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.26     0.07  1.40e-02  2.37e+01   4.9*sigma
   A 124  ALA  C
   A 125  LYS  N           1.33     1.39    -0.06  1.40e-02  2.00e+01   4.5*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.54    -0.08  1.90e-02  1.85e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.221 (Z= 11.638)
  Mean delta:    0.022 (Z=  1.170)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 122  ILE  C
   A 122  ILE  CA
   A 122  ILE  CB        111.60   146.09   -34.49  2.00e+00  2.97e+02  17.2*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50    85.52    25.98  1.70e+00  2.34e+02  15.3*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    77.05    33.95  2.80e+00  1.47e+02  12.1*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    91.50    20.00  1.70e+00  1.38e+02  11.8*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   130.19   -18.59  2.00e+00  8.64e+01   9.3*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   137.30   -15.60  1.80e+00  7.51e+01   8.7*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   134.62   -23.62  2.80e+00  7.12e+01   8.4*sigma
   A  93  LEU  CD1
   A  93  LEU  CG
   A  93  LEU  CD2       110.80   127.74   -16.94  2.20e+00  5.93e+01   7.7*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.32   -11.42  1.50e+00  5.80e+01   7.6*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50    97.62    12.88  1.70e+00  5.74e+01   7.6*sigma
   A 100  GLN  C
   A 100  GLN  CA
   A 100  GLN  CB        110.10   123.91   -13.81  1.90e+00  5.28e+01   7.3*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50    99.30    12.20  1.70e+00  5.15e+01   7.2*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   134.35   -12.65  1.80e+00  4.94e+01   7.0*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00    91.63    19.37  2.80e+00  4.79e+01   6.9*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   133.16   -11.46  1.80e+00  4.06e+01   6.4*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   132.95   -11.25  1.80e+00  3.91e+01   6.3*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   123.89   -12.29  2.00e+00  3.77e+01   6.1*sigma
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        121.70   110.87    10.83  1.80e+00  3.62e+01   6.0*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   120.39    -9.99  1.70e+00  3.45e+01   5.9*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   118.38    -5.78  1.00e+00  3.34e+01   5.8*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.94   -10.24  1.80e+00  3.24e+01   5.7*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   127.38   -11.18  2.00e+00  3.13e+01   5.6*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   123.91   -10.01  1.80e+00  3.09e+01   5.6*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.22   -10.62  2.00e+00  2.82e+01   5.3*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   131.23    -9.53  1.80e+00  2.80e+01   5.3*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   117.74    -5.14  1.00e+00  2.65e+01   5.1*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   101.85     9.55  1.90e+00  2.52e+01   5.0*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   100.56     9.54  1.90e+00  2.52e+01   5.0*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   130.66    -8.96  1.80e+00  2.48e+01   5.0*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.50    -4.90  1.00e+00  2.41e+01   4.9*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   118.49    -7.99  1.70e+00  2.21e+01   4.7*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   128.78    -7.98  1.70e+00  2.21e+01   4.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   107.02     9.18  2.00e+00  2.11e+01   4.6*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   115.78     7.22  1.60e+00  2.04e+01   4.5*sigma
   A 132  LEU  N
   A 132  LEU  CA
   A 132  LEU  C         111.00   123.46   -12.46  2.80e+00  1.98e+01   4.4*sigma
   A 100  GLN  C
   A 101  LYS  N
   A 101  LYS  CA        121.70   129.71    -8.01  1.80e+00  1.98e+01   4.4*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   129.65    -7.95  1.80e+00  1.95e+01   4.4*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   123.33   -12.33  2.80e+00  1.94e+01   4.4*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  CB        110.50   103.15     7.35  1.70e+00  1.87e+01   4.3*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00   123.05   -12.05  2.80e+00  1.85e+01   4.3*sigma
   A  83  THR  CA
   A  83  THR  CB
   A  83  THR  CG2       110.50   117.71    -7.21  1.70e+00  1.80e+01   4.2*sigma
   A  86  ILE  C
   A  86  ILE  CA
   A  86  ILE  CB        111.60   119.81    -8.21  2.00e+00  1.68e+01   4.1*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   114.36     7.34  1.80e+00  1.66e+01   4.1*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80   101.85     8.95  2.20e+00  1.65e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.90     6.90  1.70e+00  1.65e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.63e+01   4.0*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.58     4.02  1.00e+00  1.61e+01   4.0*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   128.91    -7.21  1.80e+00  1.61e+01   4.0*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   116.51    -6.01  1.50e+00  1.60e+01   4.0*sigma

  Min. delta:    0.004 (Z=  0.002)
  Max. delta:   34.486 (Z= 17.243)
  Mean delta:    3.290 (Z=  1.706)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00    49.28   130.72  5.00e+00  6.84e+02  26.1*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    81.95    98.05  5.00e+00  3.85e+02  19.6*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    85.55    94.45  5.00e+00  3.57e+02  18.9*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    93.54    86.46  5.00e+00  2.99e+02  17.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    97.11    82.89  5.00e+00  2.75e+02  16.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -106.27   -73.73  5.00e+00  2.17e+02  14.7*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   110.00    70.00  5.00e+00  1.96e+02  14.0*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   110.93    69.07  5.00e+00  1.91e+02  13.8*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   114.04    65.96  5.00e+00  1.74e+02  13.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   117.91    62.09  5.00e+00  1.54e+02  12.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -119.81   -60.19  5.00e+00  1.45e+02  12.0*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   123.35    56.65  5.00e+00  1.28e+02  11.3*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00  -129.50   -50.50  5.00e+00  1.02e+02  10.1*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -129.98   -50.02  5.00e+00  1.00e+02  10.0*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00  -131.91   -48.09  5.00e+00  9.25e+01   9.6*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   135.75    44.25  5.00e+00  7.83e+01   8.8*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -139.29   -40.71  5.00e+00  6.63e+01   8.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA          0.00    39.46   -39.46  5.00e+00  6.23e+01   7.9*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00  -147.22   -32.78  5.00e+00  4.30e+01   6.6*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   147.59    32.41  5.00e+00  4.20e+01   6.5*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -148.97   -31.03  5.00e+00  3.85e+01   6.2*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   150.29    29.71  5.00e+00  3.53e+01   5.9*sigma
   A 102  PRO  CA
   A 102  PRO  C
   A 103  ASP  N
   A 103  ASP  CA        180.00   150.96    29.04  5.00e+00  3.37e+01   5.8*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00  -151.25   -28.75  5.00e+00  3.31e+01   5.7*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   153.43    26.57  5.00e+00  2.82e+01   5.3*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   154.43    25.57  5.00e+00  2.62e+01   5.1*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -158.23   -21.77  5.00e+00  1.90e+01   4.4*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   159.33    20.67  5.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.055
  Max. delta:  130.722
  Mean delta:   21.402

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.69     5.34  2.00e-01  7.12e+02  26.7*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.53     5.04  2.00e-01  6.34e+02  25.2*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.33     4.97  2.00e-01  6.18e+02  24.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.93     3.37  2.00e-01  2.83e+02  16.8*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.03     1.48  2.00e-01  5.46e+01   7.4*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51     3.46    -0.95  2.00e-01  2.27e+01   4.8*sigma
   A  93  LEU  CG
   A  93  LEU  CB
   A  93  LEU  CD1
   A  93  LEU  CD2        -2.59    -1.67    -0.92  2.00e-01  2.11e+01   4.6*sigma

  Min. delta:    0.000
  Max. delta:    5.338
  Mean delta:    0.756

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.046
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 100  GLN  HA , Angle CB-CA-HA, observed: 96.841, delta from target: 12.159
   A 122  ILE  HA , Angle C-CA-HA, observed: 96.778, delta from target: 12.222
   A 126  VAL  HB , Angle CG2-CB-HB, observed: 120.356, delta from target: -12.356
   A 100  GLN  HA , Angle C-CA-HA, observed: 96.241, delta from target: 12.759
   A  97  SER  HA , Angle CB-CA-HA, observed: 95.533, delta from target: 13.467
   A 128  MET  HA , Angle C-CA-HA, observed: 124.036, delta from target: -14.036
   A 132  LEU  HA , Angle C-CA-HA, observed: 94.583, delta from target: 14.417
   A  79  LYS  HA , Angle CB-CA-HA, observed: 123.504, delta from target: -14.504
   A  78  ILE  HA , Angle CB-CA-HA, observed: 92.942, delta from target: 16.058
   A 126  VAL  HA , Angle CB-CA-HA, observed: 125.066, delta from target: -16.066
   A  93  LEU  HG , Angle CD2-CG-HG, observed: 91.205, delta from target: 16.795
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.130, delta from target: 16.870
   A  51  ILE  HA , Angle C-CA-HA, observed: 90.518, delta from target: 18.482
   A 131  ILE  HA , Angle N-CA-HA, observed: 128.960, delta from target: -18.960
   A 131  ILE  HA , Angle C-CA-HA, observed: 88.752, delta from target: 20.248
   A 128  MET  HA , Angle N-CA-HA, observed: 131.573, delta from target: -21.573
   A 127  ARG  HA , Angle CB-CA-HA, observed: 134.743, delta from target: -25.743
   A 127  ARG  HA , Angle N-CA-HA, observed: 83.154, delta from target: 26.846
   A 127  ARG  HA , Angle C-CA-HA, observed: 79.519, delta from target: 29.481
   A 122  ILE  HA , Angle N-CA-HA, observed: 151.047, delta from target: -41.047

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.016   0.221   2242  Z= 0.833
    Angle     :  2.934  41.047   4079  Z= 1.265
    Chirality :  0.756   5.338    176
    Planarity :  0.010   0.046    327
    Dihedral  : 17.155 130.722    769
    Min Nonbonded Distance : 1.507
  
  Molprobity Statistics.
    All-atom Clashscore : 15.78
    Ramachandran Plot:
      Outliers :  8.76 %
      Allowed  : 13.87 %
      Favored  : 77.37 %
    Rotamer:
      Outliers : 12.90 %
      Allowed  :  4.84 %
      Favored  : 82.26 %
    Cbeta Deviations : 15.15 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 16.03 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.52 (0.61), residues: 137
    helix: -1.28 (0.54), residues: 63
    sheet:  None (None), residues: 0
    loop : -3.46 (0.63), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.071   0.023   PHE A  67 
   TYR   0.098   0.016   TYR A  50 
   ARG   0.033   0.004   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.036   0.018   PHE A  67 
   TYR   0.079   0.020   TYR A 111 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================

  Time building chain proxies: 1.07, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.909, 40.116, 56.365, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   5.84 %
                favored =  79.56 %
  Rotamer outliers      =  12.90 %
  C-beta deviations     =    17
  Clashscore            =  25.70
  RMS(bonds)            =   0.0124
  RMS(angles)           =   3.09
  MolProbity score      =   3.49

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.56    -0.11  1.60e-02  4.97e+01   7.1*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.67    -0.15  2.10e-02  4.86e+01   7.0*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.62    -0.10  1.80e-02  3.08e+01   5.6*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.56    -0.10  1.90e-02  2.93e+01   5.4*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.40    -0.07  1.40e-02  2.49e+01   5.0*sigma
   A  79  LYS  CA
   A  79  LYS  CB          1.53     1.61    -0.08  2.00e-02  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.146 (Z=  7.051)
  Mean delta:    0.017 (Z=  0.908)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   141.39   -31.29  1.90e+00  2.71e+02  16.5*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   130.92   -20.42  1.50e+00  1.85e+02  13.6*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   138.37   -26.77  2.00e+00  1.79e+02  13.4*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   131.24   -21.14  1.90e+00  1.24e+02  11.1*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   129.75   -19.65  1.90e+00  1.07e+02  10.3*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   128.93   -18.83  1.90e+00  9.82e+01   9.9*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   134.76   -18.56  2.00e+00  8.61e+01   9.3*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   108.85    14.15  1.60e+00  7.82e+01   8.8*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   125.13   -14.73  1.70e+00  7.51e+01   8.7*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    96.14    14.36  1.70e+00  7.13e+01   8.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.09   -11.19  1.50e+00  5.56e+01   7.5*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   128.96   -14.86  2.00e+00  5.52e+01   7.4*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   121.06    -7.26  1.00e+00  5.28e+01   7.3*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50    99.20    12.30  1.70e+00  5.23e+01   7.2*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  CB        110.50    99.69    10.81  1.70e+00  4.04e+01   6.4*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   128.86   -12.66  2.00e+00  4.01e+01   6.3*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   132.56   -10.86  1.80e+00  3.64e+01   6.0*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.47   -10.77  1.80e+00  3.58e+01   6.0*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   124.78   -13.48  2.30e+00  3.43e+01   5.9*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   132.06   -10.36  1.80e+00  3.31e+01   5.8*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.78   -10.08  1.80e+00  3.13e+01   5.6*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   111.74     9.96  1.80e+00  3.06e+01   5.5*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.11    -5.51  1.00e+00  3.04e+01   5.5*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   105.34    10.86  2.00e+00  2.95e+01   5.4*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40   118.43    -8.03  1.50e+00  2.87e+01   5.4*sigma
   A 100  GLN  C
   A 101  LYS  N
   A 101  LYS  CA        121.70   131.04    -9.34  1.80e+00  2.69e+01   5.2*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   123.02    -9.12  1.80e+00  2.57e+01   5.1*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.51    -9.91  2.00e+00  2.45e+01   5.0*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   130.49    -8.79  1.80e+00  2.38e+01   4.9*sigma
   A  99  LEU  N
   A  99  LEU  CA
   A  99  LEU  CB        110.50   102.24     8.26  1.70e+00  2.36e+01   4.9*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   103.55     7.95  1.70e+00  2.19e+01   4.7*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   130.07    -8.37  1.80e+00  2.16e+01   4.6*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   119.27   -10.17  2.20e+00  2.14e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.01     4.59  1.00e+00  2.11e+01   4.6*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   118.82    -8.72  1.90e+00  2.10e+01   4.6*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   117.94    -7.54  1.70e+00  1.97e+01   4.4*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.02    -4.42  1.00e+00  1.95e+01   4.4*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   117.93    -7.43  1.70e+00  1.91e+01   4.4*sigma
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        121.70   129.43    -7.73  1.80e+00  1.84e+01   4.3*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   116.87    -4.27  1.00e+00  1.82e+01   4.3*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   129.29    -7.59  1.80e+00  1.78e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.27    -5.87  1.40e+00  1.76e+01   4.2*sigma
   A 119  LEU  C
   A 119  LEU  CA
   A 119  LEU  CB        110.10   118.05    -7.95  1.90e+00  1.75e+01   4.2*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   129.21    -7.51  1.80e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   117.53    -7.03  1.70e+00  1.71e+01   4.1*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   107.99     8.21  2.00e+00  1.68e+01   4.1*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   129.03    -7.33  1.80e+00  1.66e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.99     6.81  1.70e+00  1.61e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:   31.288 (Z= 16.467)
  Mean delta:    3.185 (Z=  1.726)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -59.12  -120.88  5.00e+00  5.84e+02  24.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   -65.68  -114.32  5.00e+00  5.23e+02  22.9*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    88.16    91.84  5.00e+00  3.37e+02  18.4*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   101.44    78.56  5.00e+00  2.47e+02  15.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -111.77   -68.23  5.00e+00  1.86e+02  13.6*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   120.94    59.06  5.00e+00  1.40e+02  11.8*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -137.11   -42.89  5.00e+00  7.36e+01   8.6*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA          0.00    38.40   -38.40  5.00e+00  5.90e+01   7.7*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA          0.00   -38.23    38.23  5.00e+00  5.84e+01   7.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   143.26    36.74  5.00e+00  5.40e+01   7.3*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -147.61   -32.39  5.00e+00  4.20e+01   6.5*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -148.41   -31.59  5.00e+00  3.99e+01   6.3*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -149.13   -30.87  5.00e+00  3.81e+01   6.2*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   151.77    28.23  5.00e+00  3.19e+01   5.6*sigma
   A 111  TYR  CA
   A 111  TYR  C
   A 112  VAL  N
   A 112  VAL  CA        180.00   151.93    28.07  5.00e+00  3.15e+01   5.6*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   152.08    27.92  5.00e+00  3.12e+01   5.6*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -152.19   -27.81  5.00e+00  3.09e+01   5.6*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   153.44    26.56  5.00e+00  2.82e+01   5.3*sigma
   A  70  LEU  CA
   A  70  LEU  C
   A  71  ILE  N
   A  71  ILE  CA        180.00   155.81    24.19  5.00e+00  2.34e+01   4.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA          0.00    23.17   -23.17  5.00e+00  2.15e+01   4.6*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   157.08    22.92  5.00e+00  2.10e+01   4.6*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   157.58    22.42  5.00e+00  2.01e+01   4.5*sigma
   A  71  ILE  CA
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        180.00  -159.43   -20.57  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.047
  Max. delta:  120.878
  Mean delta:   19.459

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.56     5.20  2.00e-01  6.76e+02  26.0*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.38     5.02  2.00e-01  6.31e+02  25.1*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.53     4.96  2.00e-01  6.16e+02  24.8*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.39     4.90  2.00e-01  6.01e+02  24.5*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.18     4.61  2.00e-01  5.31e+02  23.0*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -1.99     4.50  2.00e-01  5.07e+02  22.5*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -1.55     4.06  2.00e-01  4.12e+02  20.3*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.11     3.54  2.00e-01  3.13e+02  17.7*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     0.65     1.86  2.00e-01  8.67e+01   9.3*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48     1.47     1.02  2.00e-01  2.59e+01   5.1*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     1.50     1.01  2.00e-01  2.56e+01   5.1*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.69     0.82  2.00e-01  1.67e+01   4.1*sigma

  Min. delta:    0.000
  Max. delta:    5.201
  Mean delta:    1.015

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.235       0.415     1109.01  20.7*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.060       0.116       71.64   5.8*sigma
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.088       0.081      155.07   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.235
  Mean delta:    0.023

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    3" pdbres="HIS A  43  conformer  : HE2, HD1 
    3" pdbres="HIS A 134  conformer  : HE2, HD1 
    3" pdbres="HIS A 135  conformer  : HE2, HD1 
    3" pdbres="HIS A 136  conformer  : HE2, HD1 
    3" pdbres="HIS A 137  conformer  : HE2, HD1 
    3" pdbres="HIS A 138  conformer  : HE2, HD1 
    3" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 128  MET  HA , Angle C-CA-HA, observed: 97.683, delta from target: 12.317
   A  77  ILE  HA , Angle CB-CA-HA, observed: 96.150, delta from target: 12.850
   A  97  SER  HA , Angle CB-CA-HA, observed: 95.946, delta from target: 13.054
   A 124  ALA  HA , Angle N-CA-HA, observed: 123.822, delta from target: -13.822
   A  77  ILE  HB , Angle CA-CB-HB, observed: 93.871, delta from target: 15.129
   A  51  ILE  HA , Angle CB-CA-HA, observed: 93.471, delta from target: 15.529
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.447, delta from target: 15.553
   A  77  ILE  HA , Angle C-CA-HA, observed: 92.273, delta from target: 16.727
   A  99  LEU  HA , Angle N-CA-HA, observed: 128.083, delta from target: -18.083
   A 128  MET  HA , Angle N-CA-HA, observed: 128.653, delta from target: -18.653
   A  89  TYR  HA , Angle C-CA-HA, observed: 85.551, delta from target: 23.449
   A  89  TYR  HA , Angle N-CA-HA, observed: 133.628, delta from target: -23.628
   A  77  ILE  HA , Angle N-CA-HA, observed: 135.903, delta from target: -25.903
   A  79  LYS  HA , Angle N-CA-HA, observed: 139.317, delta from target: -29.317
   A 124  ALA  HA , Angle CB-CA-HA, observed: 76.520, delta from target: 32.480
   A  79  LYS  HA , Angle C-CA-HA, observed: 73.457, delta from target: 35.543
   A  89  TYR  HA , Angle CB-CA-HA, observed: 71.385, delta from target: 37.615

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.146   2242  Z= 0.647
    Angle     :  2.904  37.615   4079  Z= 1.279
    Chirality :  1.015   5.201    176
    Planarity :  0.017   0.231    327
    Dihedral  : 16.081 120.878    769
    Min Nonbonded Distance : 1.461
  
  Molprobity Statistics.
    All-atom Clashscore : 25.70
    Ramachandran Plot:
      Outliers :  8.76 %
      Allowed  : 12.41 %
      Favored  : 78.83 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  9.68 %
      Favored  : 84.68 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 9.92 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.82 (0.66), residues: 137
    helix: -2.42 (0.51), residues: 63
    sheet:  None (None), residues: 0
    loop : -2.68 (0.77), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.004   HIS A  43 
   PHE   0.093   0.024   PHE A  15 
   TYR   0.523   0.047   TYR A  91 
   ARG   0.054   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.004   HIS A  43 
   PHE   0.061   0.025   PHE A  15 
   TYR   0.415   0.054   TYR A  91 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   8.76 %
                favored =  77.37 %
  Rotamer outliers      =  12.90 %
  C-beta deviations     =    20
  Clashscore            =  15.78
  RMS(bonds)            =   0.0159
  RMS(angles)           =   2.93
  MolProbity score      =   3.31

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Time building chain proxies: 1.19, per 1000 atoms: 0.54
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.789, 65.002, 62.575, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   8.76 %
                favored =  78.83 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =    14
  Clashscore            =  25.70
  RMS(bonds)            =   0.0123
  RMS(angles)           =   2.90
  MolProbity score      =   3.22

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.74    -0.22  2.10e-02  1.07e+02  10.4*sigma
   A 125  LYS  N
   A 125  LYS  CA          1.46     1.62    -0.16  1.90e-02  7.29e+01   8.5*sigma
   A 124  ALA  C
   A 125  LYS  N           1.33     1.44    -0.11  1.40e-02  6.29e+01   7.9*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.57    -0.12  1.60e-02  5.73e+01   7.6*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.60    -0.14  1.90e-02  5.69e+01   7.5*sigma
   A 129  ARG  N
   A 129  ARG  CA          1.46     1.60    -0.14  1.90e-02  5.60e+01   7.5*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.60    -0.14  1.90e-02  5.28e+01   7.3*sigma
   A 127  ARG  C
   A 128  MET  N           1.33     1.41    -0.09  1.40e-02  3.75e+01   6.1*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.24     0.08  1.40e-02  3.67e+01   6.1*sigma
   A  92  THR  CA
   A  92  THR  C           1.52     1.40     0.12  2.10e-02  3.49e+01   5.9*sigma
   A  93  LEU  N
   A  93  LEU  CA          1.46     1.35     0.11  1.90e-02  3.31e+01   5.8*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.62    -0.10  1.80e-02  3.22e+01   5.7*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.56    -0.10  1.90e-02  2.83e+01   5.3*sigma
   A 127  ARG  CA
   A 127  ARG  C           1.52     1.63    -0.11  2.10e-02  2.74e+01   5.2*sigma
   A 125  LYS  CA
   A 125  LYS  C           1.52     1.42     0.11  2.10e-02  2.55e+01   5.0*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.55    -0.10  1.90e-02  2.50e+01   5.0*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     1.55    -0.09  1.90e-02  2.44e+01   4.9*sigma
   A  94  GLY  N
   A  94  GLY  CA          1.45     1.37     0.08  1.60e-02  2.39e+01   4.9*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.62    -0.09  2.10e-02  1.85e+01   4.3*sigma
   A  91  TYR  N
   A  91  TYR  CA          1.46     1.38     0.08  1.90e-02  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.218 (Z= 10.362)
  Mean delta:    0.022 (Z=  1.158)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70    86.94    34.76  1.80e+00  3.73e+02  19.3*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    69.99    41.01  2.80e+00  2.15e+02  14.6*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   132.97   -22.87  1.90e+00  1.45e+02  12.0*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20    94.89    21.31  2.00e+00  1.14e+02  10.7*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   103.18    18.52  1.80e+00  1.06e+02  10.3*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   130.46   -19.06  1.90e+00  1.01e+02  10.0*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   138.58   -16.88  1.80e+00  8.79e+01   9.4*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   137.07   -15.37  1.80e+00  7.29e+01   8.5*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40    97.83    12.57  1.50e+00  7.02e+01   8.4*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50    98.59    12.91  1.70e+00  5.77e+01   7.6*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   135.14   -13.44  1.80e+00  5.57e+01   7.5*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   109.34    12.36  1.80e+00  4.72e+01   6.9*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   125.17   -13.57  2.00e+00  4.60e+01   6.8*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00    92.23    18.77  2.80e+00  4.50e+01   6.7*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   121.77   -11.37  1.70e+00  4.47e+01   6.7*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   133.51   -11.81  1.80e+00  4.30e+01   6.6*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50    99.59    10.91  1.70e+00  4.11e+01   6.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   133.02   -11.32  1.80e+00  3.95e+01   6.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.66   -10.96  1.80e+00  3.71e+01   6.1*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.64   -10.94  1.80e+00  3.69e+01   6.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   126.00    -9.10  1.50e+00  3.68e+01   6.1*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   104.43    11.77  2.00e+00  3.46e+01   5.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   130.73    -9.93  1.70e+00  3.41e+01   5.8*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   120.28    -9.78  1.70e+00  3.31e+01   5.8*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   120.82   -10.72  1.90e+00  3.18e+01   5.6*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   131.61    -9.91  1.80e+00  3.03e+01   5.5*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.40   -10.80  2.00e+00  2.92e+01   5.4*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   131.09    -9.39  1.80e+00  2.72e+01   5.2*sigma
   A 129  ARG  C
   A 129  ARG  CA
   A 129  ARG  CB        110.10   100.29     9.81  1.90e+00  2.66e+01   5.2*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   119.64    -9.54  1.90e+00  2.52e+01   5.0*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   130.69    -8.99  1.80e+00  2.49e+01   5.0*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N         116.20   125.96    -9.76  2.00e+00  2.38e+01   4.9*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   124.64   -13.64  2.80e+00  2.37e+01   4.9*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   124.89     6.31  1.30e+00  2.36e+01   4.9*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.81     4.79  1.00e+00  2.30e+01   4.8*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.39    -4.79  1.00e+00  2.30e+01   4.8*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00   124.05   -13.05  2.80e+00  2.17e+01   4.7*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   123.09    -8.99  2.00e+00  2.02e+01   4.5*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.03    -4.43  1.00e+00  1.96e+01   4.4*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   118.19    -4.39  1.00e+00  1.92e+01   4.4*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N         116.20   107.50     8.70  2.00e+00  1.89e+01   4.4*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  C         111.00   123.16   -12.16  2.80e+00  1.88e+01   4.3*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   124.68    -8.48  2.00e+00  1.80e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   114.10     7.60  1.80e+00  1.78e+01   4.2*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   117.59    -7.09  1.70e+00  1.74e+01   4.2*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N         116.20   107.90     8.30  2.00e+00  1.72e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N         116.20   108.07     8.13  2.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   41.010 (Z= 19.313)
  Mean delta:    3.382 (Z=  1.755)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    59.62   120.38  5.00e+00  5.80e+02  24.1*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   -71.23  -108.77  5.00e+00  4.73e+02  21.8*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00    73.78   106.22  5.00e+00  4.51e+02  21.2*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    75.92   104.08  5.00e+00  4.33e+02  20.8*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   103.91    76.09  5.00e+00  2.32e+02  15.2*sigma
   A  46  SER  CA
   A  46  SER  C
   A  47  ASP  N
   A  47  ASP  CA        180.00   112.71    67.29  5.00e+00  1.81e+02  13.5*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   113.32    66.68  5.00e+00  1.78e+02  13.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   115.18    64.82  5.00e+00  1.68e+02  13.0*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   115.91    64.09  5.00e+00  1.64e+02  12.8*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   120.74    59.26  5.00e+00  1.40e+02  11.9*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -128.04   -51.96  5.00e+00  1.08e+02  10.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   129.68    50.32  5.00e+00  1.01e+02  10.1*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -130.45   -49.55  5.00e+00  9.82e+01   9.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA          0.00   -35.49    35.49  5.00e+00  5.04e+01   7.1*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -146.43   -33.57  5.00e+00  4.51e+01   6.7*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00   149.06    30.94  5.00e+00  3.83e+01   6.2*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   152.45    27.55  5.00e+00  3.04e+01   5.5*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA          0.00    26.96   -26.96  5.00e+00  2.91e+01   5.4*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -153.29   -26.71  5.00e+00  2.85e+01   5.3*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   154.80    25.20  5.00e+00  2.54e+01   5.0*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   155.83    24.17  5.00e+00  2.34e+01   4.8*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   156.11    23.89  5.00e+00  2.28e+01   4.8*sigma
   A  45  PHE  CA
   A  45  PHE  C
   A  46  SER  N
   A  46  SER  CA        180.00   156.14    23.86  5.00e+00  2.28e+01   4.8*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   156.36    23.64  5.00e+00  2.24e+01   4.7*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA          0.00   -23.48    23.48  5.00e+00  2.21e+01   4.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   158.39    21.61  5.00e+00  1.87e+01   4.3*sigma
   A  71  ILE  CA
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        180.00   158.94    21.06  5.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.005
  Max. delta:  120.378
  Mean delta:   20.964

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.24     5.75  2.00e-01  8.26e+02  28.7*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.67     5.32  2.00e-01  7.07e+02  26.6*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.57     5.08  2.00e-01  6.46e+02  25.4*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.61     5.05  2.00e-01  6.37e+02  25.2*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.48     4.99  2.00e-01  6.23e+02  25.0*sigma
   A 130  SER  CA
   A 130  SER  N
   A 130  SER  C
   A 130  SER  CB          2.51    -1.92     4.43  2.00e-01  4.92e+02  22.2*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -1.98     4.42  2.00e-01  4.88e+02  22.1*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -1.84     4.35  2.00e-01  4.73e+02  21.8*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.90     3.34  2.00e-01  2.78e+02  16.7*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -0.68     3.11  2.00e-01  2.43e+02  15.6*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     0.08     2.43  2.00e-01  1.48e+02  12.2*sigma

  Min. delta:    0.000
  Max. delta:    5.748
  Mean delta:    1.135

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.060       0.106       71.51   5.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O
   A 124  ALA  N             0.055       0.095       30.42   4.8*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.091       0.094      167.01   4.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O
   A  78  ILE  N             0.053       0.092       28.30   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.091
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 124  ALA  HA , Angle CB-CA-HA, observed: 121.645, delta from target: -12.645
   A 124  ALA  HA , Angle C-CA-HA, observed: 95.387, delta from target: 13.613
   A  78  ILE  HA , Angle CB-CA-HA, observed: 94.281, delta from target: 14.719
   A 130  SER  HA , Angle N-CA-HA, observed: 94.284, delta from target: 15.716
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.242, delta from target: 15.758
   A 129  ARG  HA , Angle N-CA-HA, observed: 93.396, delta from target: 16.604
   A 127  ARG  HA , Angle C-CA-HA, observed: 91.928, delta from target: 17.072
   A 127  ARG  H  , Angle CA-N-H, observed: 131.091, delta from target: -17.091
   A 127  ARG  H  , Angle C-N-H, observed: 141.972, delta from target: -17.672
   A 122  ILE  HA , Angle C-CA-HA, observed: 88.900, delta from target: 20.100
   A  51  ILE  HA , Angle CB-CA-HA, observed: 88.596, delta from target: 20.404
   A  78  ILE  HA , Angle C-CA-HA, observed: 74.141, delta from target: 34.859
   A 126  VAL  HA , Angle N-CA-HA, observed: 145.651, delta from target: -35.651
   A  89  TYR  HA , Angle CB-CA-HA, observed: 70.159, delta from target: 38.841
   A  89  TYR  HA , Angle C-CA-HA, observed: 63.359, delta from target: 45.641
   A  89  TYR  HA , Angle N-CA-HA, observed: 172.716, delta from target: -62.716

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.015   0.218   2242  Z= 0.824
    Angle     :  3.209  62.716   4079  Z= 1.352
    Chirality :  1.135   5.748    176
    Planarity :  0.013   0.088    327
    Dihedral  : 16.768 120.378    769
    Min Nonbonded Distance : 1.533
  
  Molprobity Statistics.
    All-atom Clashscore : 20.29
    Ramachandran Plot:
      Outliers : 10.22 %
      Allowed  : 10.22 %
      Favored  : 79.56 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  6.45 %
      Favored  : 87.10 %
    Cbeta Deviations : 12.88 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 12.21 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.84 (0.64), residues: 137
    helix: -2.61 (0.51), residues: 74
    sheet:  None (None), residues: 0
    loop : -2.36 (0.75), residues: 63
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.004   HIS A  43 
   PHE   0.122   0.022   PHE A  15 
   TYR   0.227   0.023   TYR A  91 
   ARG   0.024   0.005   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.004   HIS A  43 
   PHE   0.082   0.021   PHE A  15 
   TYR   0.177   0.027   TYR A  91 
   ARG   0.002   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  14" pdb=" CB  GLU A  84 "
        model="  14" pdb=" CB  LYS A  85 "
        model="  14" pdb=" CB  ILE A  86 "
  Number of C-beta restraints generated:  258

  Time building geometry restraints manager: 0.74 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" CZ  ARG A 129 "
       model="  14" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.24e+00
  bond model="  14" pdb=" CZ  ARG A  21 "
       model="  14" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.47e+00
  bond model="  14" pdb=" CD2 HIS A 139 "
       model="  14" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.71e+00
  bond model="  14" pdb=" ND1 HIS A 136 "
       model="  14" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.32e+00
  bond model="  14" pdb=" CZ  ARG A  58 "
       model="  14" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.29e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       95.68 -   102.91: 14
      102.91 -   110.14: 2127
      110.14 -   117.38: 926
      117.38 -   124.61: 918
      124.61 -   131.84: 94
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" CA  ILE A  86 "
        model="  14" pdb=" CB  ILE A  86 "
        model="  14" pdb=" CG1 ILE A  86 "
      ideal   model   delta    sigma   weight residual
     110.40  120.90  -10.50 1.70e+00 3.46e-01 3.82e+01
  angle model="  14" pdb=" C   LYS A  85 "
        model="  14" pdb=" N   ILE A  86 "
        model="  14" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  131.84  -10.14 1.80e+00 3.09e-01 3.17e+01
  angle model="  14" pdb=" C   ILE A 122 "
        model="  14" pdb=" N   GLU A 123 "
        model="  14" pdb=" CA  GLU A 123 "
      ideal   model   delta    sigma   weight residual
     121.70  130.27   -8.57 1.80e+00 3.09e-01 2.27e+01
  angle model="  14" pdb=" C   GLU A  84 "
        model="  14" pdb=" N   LYS A  85 "
        model="  14" pdb=" CA  LYS A  85 "
      ideal   model   delta    sigma   weight residual
     121.70  130.02   -8.32 1.80e+00 3.09e-01 2.14e+01
  angle model="  14" pdb=" C   ILE A  86 "
        model="  14" pdb=" CA  ILE A  86 "
        model="  14" pdb=" HA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     109.00   95.68   13.32 3.00e+00 1.11e-01 1.97e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 927
       17.86 -    35.72: 61
       35.72 -    53.58: 22
       53.58 -    71.44: 10
       71.44 -    89.30: 7
  Dihedral angle restraints: 1027
    sinusoidal: 562
      harmonic: 465
  Sorted by residual:
  dihedral model="  14" pdb=" CA  ASP A 118 "
           model="  14" pdb=" C   ASP A 118 "
           model="  14" pdb=" N   LEU A 119 "
           model="  14" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.94   28.06     0      5.00e+00 4.00e-02 3.15e+01
  dihedral model="  14" pdb=" CA  GLU A 123 "
           model="  14" pdb=" C   GLU A 123 "
           model="  14" pdb=" N   ALA A 124 "
           model="  14" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.28  -27.72     0      5.00e+00 4.00e-02 3.07e+01
  dihedral model="  14" pdb=" CA  LEU A  93 "
           model="  14" pdb=" C   LEU A  93 "
           model="  14" pdb=" N   GLY A  94 "
           model="  14" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.42   23.58     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 1024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.944: 173
       0.944 -    1.887: 0
       1.887 -    2.831: 0
       2.831 -    3.774: 0
       3.774 -    4.717: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CA  LYS A  85 "
            model="  14" pdb=" N   LYS A  85 "
            model="  14" pdb=" C   LYS A  85 "
            model="  14" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.21    4.72 2.00e-01 2.50e+01 5.56e+02
  chirality model="  14" pdb=" CA  GLU A  84 "
            model="  14" pdb=" N   GLU A  84 "
            model="  14" pdb=" C   GLU A  84 "
            model="  14" pdb=" CB  GLU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.97    4.48 2.00e-01 2.50e+01 5.03e+02
  chirality model="  14" pdb=" CA  ILE A  86 "
            model="  14" pdb=" N   ILE A  86 "
            model="  14" pdb=" C   ILE A  86 "
            model="  14" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -1.73    4.17 2.00e-01 2.50e+01 4.34e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A 111 "    0.182 2.00e-02 2.50e+03   7.63e-02 1.75e+02
        model="  14" pdb=" CG  TYR A 111 "   -0.043 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A 111 "   -0.026 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A 111 "   -0.060 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A 111 "   -0.031 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A 111 "    0.106 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A 111 "   -0.114 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A 111 "   -0.055 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A 111 "    0.047 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  91 "    0.155 2.00e-02 2.50e+03   5.97e-02 1.07e+02
        model="  14" pdb=" CG  TYR A  91 "   -0.023 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  91 "   -0.037 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  91 "   -0.035 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  91 "    0.018 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  91 "    0.084 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  91 "   -0.066 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  91 "   -0.059 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  91 "   -0.006 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  91 "   -0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  12 "    0.121 2.00e-02 2.50e+03   5.77e-02 9.99e+01
        model="  14" pdb=" CG  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  12 "   -0.026 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  12 "   -0.027 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  12 "    0.131 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  12 "   -0.048 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  12 "   -0.032 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  12 "   -0.025 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  12 "   -0.040 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.36: 681
        2.36 -     2.92: 5003
        2.92 -     3.48: 5303
        3.48 -     4.04: 6889
        4.04 -     4.60: 10166
  Nonbonded interactions: 28042
  Sorted by model distance:
  nonbonded model="  14" pdb=" OE2 GLU A  16 "
            model="  14" pdb=" HZ2 LYS A  19 "
     model   vdw
     1.804 1.850
  nonbonded model="  14" pdb=" H   ILE A 108 "
            model="  14" pdb="HG12 ILE A 108 "
     model   vdw
     1.813 2.270
  nonbonded model="  14" pdb=" OD1 ASP A  44 "
            model="  14" pdb=" HG  SER A  46 "
     model   vdw
     1.829 1.850
  nonbonded model="  14" pdb=" HG  SER A  17 "
            model="  14" pdb=" O   SER A  76 "
     model   vdw
     1.831 1.850
  nonbonded model="  14" pdb=" HZ3 LYS A  10 "
            model="  14" pdb=" OD1 ASP A  23 "
     model   vdw
     1.837 1.850
  ... (remaining 28037 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =  10.22 %
                favored =  79.56 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    17
  Clashscore            =  20.29
  RMS(bonds)            =   0.0154
  RMS(angles)           =   3.21
  MolProbity score      =   3.16

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2200
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 130}

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.628, 51.171, 48.996, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.12, per 1000 atoms: 0.51
  Number of scatterers: 2200
  At special positions: 0
  Unit cell: (61.13, 82.433, 54.012, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1088      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Bonds with excessive lengths:
    Distance model: 87.6916 (ideal: 1.231)
      ATOM   2186  C   HIS A 139      21.953  52.419  -7.087  1.00 71.95           C
      ATOM   2194  OXT HIS A 139     -23.332 -20.559 -24.787  1.00 55.79           O

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  12" pdb=" CB  LEU A  93 "
  Number of C-beta restraints generated:  262

  Time building geometry restraints manager: 0.90 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 98
        1.23 -     1.43: 374
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" CD2 HIS A 138 "
       model="  12" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.406 -0.032 1.10e-02 8.26e+03 8.45e+00
  bond model="  12" pdb=" CD2 HIS A 136 "
       model="  12" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.35e+00
  bond model="  12" pdb=" CZ  ARG A  21 "
       model="  12" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.97e+00
  bond model="  12" pdb=" CD2 HIS A 139 "
       model="  12" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.33e+00
  bond model="  12" pdb=" CD2 HIS A 134 "
       model="  12" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.94e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       94.07 -   101.37: 8
      101.37 -   108.67: 729
      108.67 -   115.97: 2259
      115.97 -   123.27: 872
      123.27 -   130.56: 211
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" OE1 GLN A  66 "
        model="  12" pdb=" CD  GLN A  66 "
        model="  12" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.19    5.41 1.00e+00 1.00e+00 2.93e+01
  angle model="  12" pdb=" C   LEU A  93 "
        model="  12" pdb=" CA  LEU A  93 "
        model="  12" pdb=" HA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     109.00   94.07   14.93 3.00e+00 1.11e-01 2.48e+01
  angle model="  12" pdb=" C   THR A  92 "
        model="  12" pdb=" N   LEU A  93 "
        model="  12" pdb=" CA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     121.70  130.49   -8.79 1.80e+00 3.09e-01 2.39e+01
  angle model="  12" pdb=" OE1 GLN A 100 "
        model="  12" pdb=" CD  GLN A 100 "
        model="  12" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  117.87    4.73 1.00e+00 1.00e+00 2.23e+01
  angle model="  12" pdb=" N   LEU A  93 "
        model="  12" pdb=" CA  LEU A  93 "
        model="  12" pdb=" C   LEU A  93 "
      ideal   model   delta    sigma   weight residual
     111.00  124.22  -13.22 2.80e+00 1.28e-01 2.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 920
       17.58 -    35.17: 70
       35.17 -    52.75: 37
       52.75 -    70.33: 2
       70.33 -    87.91: 2
  Dihedral angle restraints: 1031
    sinusoidal: 562
      harmonic: 469
  Sorted by residual:
  dihedral model="  12" pdb=" CA  GLU A 120 "
           model="  12" pdb=" C   GLU A 120 "
           model="  12" pdb=" N   GLY A 121 "
           model="  12" pdb=" CA  GLY A 121 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -135.97  -44.03     0      5.00e+00 4.00e-02 7.75e+01
  dihedral model="  12" pdb=" CA  THR A  92 "
           model="  12" pdb=" C   THR A  92 "
           model="  12" pdb=" N   LEU A  93 "
           model="  12" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.08   41.92     0      5.00e+00 4.00e-02 7.03e+01
  dihedral model="  12" pdb=" CA  ASP A 103 "
           model="  12" pdb=" C   ASP A 103 "
           model="  12" pdb=" N   VAL A 104 "
           model="  12" pdb=" CA  VAL A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.49  -35.51     0      5.00e+00 4.00e-02 5.04e+01
  ... (remaining 1028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.885: 175
       0.885 -    1.768: 0
       1.768 -    2.652: 0
       2.652 -    3.536: 0
       3.536 -    4.420: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  LEU A  93 "
            model="  12" pdb=" N   LEU A  93 "
            model="  12" pdb=" C   LEU A  93 "
            model="  12" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.91    4.42 2.00e-01 2.50e+01 4.88e+02
  chirality model="  12" pdb=" CA  LEU A 107 "
            model="  12" pdb=" N   LEU A 107 "
            model="  12" pdb=" C   LEU A 107 "
            model="  12" pdb=" CB  LEU A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality model="  12" pdb=" CB  ILE A  71 "
            model="  12" pdb=" CA  ILE A  71 "
            model="  12" pdb=" CG1 ILE A  71 "
            model="  12" pdb=" CG2 ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.12e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  89 "    0.257 2.00e-02 2.50e+03   1.10e-01 3.60e+02
        model="  12" pdb=" CG  TYR A  89 "   -0.022 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  89 "   -0.054 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  89 "   -0.054 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  89 "   -0.039 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  89 "   -0.033 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  89 "    0.218 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  89 "   -0.084 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  89 "   -0.088 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  89 "   -0.063 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  89 "   -0.051 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  PHE A  45 "    0.202 2.00e-02 2.50e+03   9.04e-02 2.45e+02
        model="  12" pdb=" CG  PHE A  45 "   -0.022 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 PHE A  45 "   -0.053 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 PHE A  45 "   -0.039 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 PHE A  45 "   -0.014 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 PHE A  45 "   -0.027 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  PHE A  45 "    0.059 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 PHE A  45 "   -0.100 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 PHE A  45 "   -0.057 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 PHE A  45 "   -0.037 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 PHE A  45 "   -0.078 2.00e-02 2.50e+03
        model="  12" pdb=" HZ  PHE A  45 "    0.165 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  50 "   -0.233 2.00e-02 2.50e+03   8.81e-02 2.33e+02
        model="  12" pdb=" CG  TYR A  50 "    0.046 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  50 "    0.063 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  50 "    0.049 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  50 "   -0.101 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  50 "    0.114 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  50 "    0.075 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.34: 516
        2.34 -     2.90: 5067
        2.90 -     3.47: 5296
        3.47 -     4.03: 6581
        4.03 -     4.60: 9936
  Nonbonded interactions: 27396
  Sorted by model distance:
  nonbonded model="  12" pdb="HG23 VAL A  41 "
            model="  12" pdb=" H   HIS A  43 "
     model   vdw
     1.773 2.270
  nonbonded model="  12" pdb=" HZ2 LYS A  10 "
            model="  12" pdb=" OD1 ASP A  23 "
     model   vdw
     1.777 1.850
  nonbonded model="  12" pdb=" OD2 ASP A  44 "
            model="  12" pdb=" HG  SER A  46 "
     model   vdw
     1.799 1.850
  nonbonded model="  12" pdb=" O   LYS A  63 "
            model="  12" pdb=" HH  TYR A  89 "
     model   vdw
     1.807 1.850
  nonbonded model="  12" pdb="HG11 VAL A  41 "
            model="  12" pdb=" HB  ILE A 108 "
     model   vdw
     1.809 2.440
  ... (remaining 27391 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.07 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 129}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 69
        1.23 -     1.42: 403
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" CD2 HIS A 137 "
       model="  14" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.66e+00
  bond model="  14" pdb=" CZ  ARG A  21 "
       model="  14" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.89e+00
  bond model="  14" pdb=" CD2 HIS A  43 "
       model="  14" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.48e+00
  bond model="  14" pdb=" CD2 HIS A 135 "
       model="  14" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.10e+00
  bond model="  14" pdb=" CE1 HIS A  43 "
       model="  14" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.01e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.46 -   105.37: 66
      105.37 -   111.28: 2400
      111.28 -   117.18: 596
      117.18 -   123.09: 786
      123.09 -   129.00: 231
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" OE1 GLN A  66 "
        model="  14" pdb=" CD  GLN A  66 "
        model="  14" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.44    5.16 1.00e+00 1.00e+00 2.66e+01
  angle model="  14" pdb=" OE1 GLN A 100 "
        model="  14" pdb=" CD  GLN A 100 "
        model="  14" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  117.98    4.62 1.00e+00 1.00e+00 2.13e+01
  angle model="  14" pdb=" CA  HIS A 137 "
        model="  14" pdb=" CB  HIS A 137 "
        model="  14" pdb=" CG  HIS A 137 "
      ideal   model   delta    sigma   weight residual
     113.80  118.24   -4.44 1.00e+00 1.00e+00 1.97e+01
  angle model="  14" pdb=" CA  ASP A  29 "
        model="  14" pdb=" CB  ASP A  29 "
        model="  14" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.70   -4.10 1.00e+00 1.00e+00 1.68e+01
  angle model="  14" pdb=" N   PRO A 114 "
        model="  14" pdb=" CA  PRO A 114 "
        model="  14" pdb=" CB  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     103.00  107.50   -4.50 1.10e+00 8.26e-01 1.67e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 938
       17.64 -    35.28: 72
       35.28 -    52.93: 12
       52.93 -    70.57: 6
       70.57 -    88.21: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  14" pdb=" CA  HIS A 138 "
           model="  14" pdb=" C   HIS A 138 "
           model="  14" pdb=" N   HIS A 139 "
           model="  14" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.04   45.96     0      5.00e+00 4.00e-02 8.45e+01
  dihedral model="  14" pdb=" C   ILE A 108 "
           model="  14" pdb=" N   ILE A 108 "
           model="  14" pdb=" CA  ILE A 108 "
           model="  14" pdb=" CB  ILE A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.48   15.48     0      2.50e+00 1.60e-01 3.83e+01
  dihedral model="  14" pdb=" CA  HIS A 135 "
           model="  14" pdb=" C   HIS A 135 "
           model="  14" pdb=" N   HIS A 136 "
           model="  14" pdb=" CA  HIS A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.80   29.20     0      5.00e+00 4.00e-02 3.41e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.093: 118
       0.093 -    0.184: 51
       0.184 -    0.276: 5
       0.276 -    0.368: 1
       0.368 -    0.459: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CA  ILE A 108 "
            model="  14" pdb=" N   ILE A 108 "
            model="  14" pdb=" C   ILE A 108 "
            model="  14" pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.97    0.46 2.00e-01 2.50e+01 5.28e+00
  chirality model="  14" pdb=" CB  ILE A  71 "
            model="  14" pdb=" CA  ILE A  71 "
            model="  14" pdb=" CG1 ILE A  71 "
            model="  14" pdb=" CG2 ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.71e+00
  chirality model="  14" pdb=" CA  PRO A  54 "
            model="  14" pdb=" N   PRO A  54 "
            model="  14" pdb=" C   PRO A  54 "
            model="  14" pdb=" CB  PRO A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.60e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A 111 "    0.282 2.00e-02 2.50e+03   1.14e-01 3.92e+02
        model="  14" pdb=" CG  TYR A 111 "   -0.074 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A 111 "   -0.097 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A 111 "   -0.047 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A 111 "    0.029 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A 111 "    0.052 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A 111 "    0.063 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A 111 "   -0.195 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A 111 "   -0.050 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A 111 "    0.097 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A 111 "   -0.044 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  89 "   -0.109 2.00e-02 2.50e+03   1.01e-01 3.08e+02
        model="  14" pdb=" CG  TYR A  89 "   -0.108 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  89 "    0.035 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  89 "    0.055 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  89 "    0.005 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  89 "   -0.076 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  89 "   -0.171 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  89 "    0.152 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  89 "    0.188 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  89 "    0.039 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  50 "   -0.224 2.00e-02 2.50e+03   9.34e-02 2.61e+02
        model="  14" pdb=" CG  TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  50 "    0.046 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  50 "    0.049 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  50 "   -0.172 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  50 "    0.080 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  50 "    0.090 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  50 "    0.048 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  50 "    0.039 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 401
        2.32 -     2.89: 5044
        2.89 -     3.46: 5015
        3.46 -     4.03: 6341
        4.03 -     4.60: 9389
  Nonbonded interactions: 26190
  Sorted by model distance:
  nonbonded model="  14" pdb=" OE2 GLU A  24 "
            model="  14" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.752 1.850
  nonbonded model="  14" pdb=" OD2 ASP A  36 "
            model="  14" pdb=" HZ2 LYS A  40 "
     model   vdw
     1.754 1.850
  nonbonded model="  14" pdb=" OD2 ASP A  44 "
            model="  14" pdb=" HG  SER A  46 "
     model   vdw
     1.804 1.850
  nonbonded model="  14" pdb=" HE  ARG A  21 "
            model="  14" pdb=" OD2 ASP A  29 "
     model   vdw
     1.873 1.850
  nonbonded model="  14" pdb=" O   ILE A  30 "
            model="  14" pdb=" HG1 THR A  34 "
     model   vdw
     1.888 1.850
  ... (remaining 26185 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.092, 44.039, 66.006, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 0.92, per 1000 atoms: 0.41
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (68.642, 73.966, 39.647, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  PRO A  52 "
        model="   1" pdb=" CB  ILE A  77 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CB  TYR A  89 "
        model="   1" pdb=" CB  THR A  92 "
        model="   1" pdb=" CB  LEU A  93 "
        model="   1" pdb=" CB  SER A  97 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.25 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.765, 58.715, 52.272, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 49
        1.23 -     1.43: 423
        1.43 -     1.62: 658
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   1" pdb=" N   LYS A  79 "
       model="   1" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.654 -0.196 1.90e-02 2.77e+03 1.07e+02
  bond model="   1" pdb=" CA  ILE A  78 "
       model="   1" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.711 -0.186 2.10e-02 2.27e+03 7.84e+01
  bond model="   1" pdb=" C   ILE A  78 "
       model="   1" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.441 -0.112 1.40e-02 5.10e+03 6.37e+01
  bond model="   1" pdb=" N   GLY A  80 "
       model="   1" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.570 -0.119 1.60e-02 3.91e+03 5.56e+01
  bond model="   1" pdb=" C   LEU A  93 "
       model="   1" pdb=" N   GLY A  94 "
    ideal  model  delta    sigma   weight residual
    1.329  1.242  0.087 1.40e-02 5.10e+03 3.83e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       89.74 -    99.78: 15
       99.78 -   109.82: 2051
      109.82 -   119.86: 1215
      119.86 -   129.90: 788
      129.90 -   139.94: 10
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   1" pdb=" C   ILE A  78 "
        model="   1" pdb=" CA  ILE A  78 "
        model="   1" pdb=" CB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     111.60  137.68  -26.08 2.00e+00 2.50e-01 1.70e+02
  angle model="   1" pdb=" N   ILE A  78 "
        model="   1" pdb=" CA  ILE A  78 "
        model="   1" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.00  139.94  -29.94 3.00e+00 1.11e-01 9.96e+01
  angle model="   1" pdb=" C   ASP A  88 "
        model="   1" pdb=" N   TYR A  89 "
        model="   1" pdb=" CA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     121.70  136.57  -14.87 1.80e+00 3.09e-01 6.82e+01
  angle model="   1" pdb=" N   ILE A  78 "
        model="   1" pdb=" CA  ILE A  78 "
        model="   1" pdb=" CB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     111.50   97.65   13.85 1.70e+00 3.46e-01 6.63e+01
  angle model="   1" pdb=" O   GLY A  94 "
        model="   1" pdb=" C   GLY A  94 "
        model="   1" pdb=" N   ASP A  95 "
      ideal   model   delta    sigma   weight residual
     123.00  110.15   12.85 1.60e+00 3.91e-01 6.45e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.35: 958
       22.35 -    44.70: 41
       44.70 -    67.05: 13
       67.05 -    89.39: 4
       89.39 -   111.74: 1
  Dihedral angle restraints: 1017
    sinusoidal: 562
      harmonic: 455
  Sorted by residual:
  dihedral model="   1" pdb=" CA  ILE A  77 "
           model="   1" pdb=" C   ILE A  77 "
           model="   1" pdb=" N   ILE A  78 "
           model="   1" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -68.26 -111.74     0      5.00e+00 4.00e-02 4.99e+02
  dihedral model="   1" pdb=" CA  THR A  92 "
           model="   1" pdb=" C   THR A  92 "
           model="   1" pdb=" N   LEU A  93 "
           model="   1" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -116.09  -63.91     0      5.00e+00 4.00e-02 1.63e+02
  dihedral model="   1" pdb=" CA  GLY A  80 "
           model="   1" pdb=" C   GLY A  80 "
           model="   1" pdb=" N   TYR A  81 "
           model="   1" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  120.78   59.22     0      5.00e+00 4.00e-02 1.40e+02
  ... (remaining 1014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.215: 167
       1.215 -    2.430: 0
       2.430 -    3.645: 0
       3.645 -    4.860: 4
       
============================== Collecting inputs ==============================

4.860 -    6.075: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  LYS A  79 "
            model="   1" pdb=" N   LYS A  79 "
            model="   1" pdb=" C   LYS A  79 "
            model="   1" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.56    6.07 2.00e-01 2.50e+01 9.23e+02
  chirality model="   1" pdb=" CA  LEU A  93 "
            model="   1" pdb=" N   LEU A  93 "
            model="   1" pdb=" C   LEU A  93 "
            model="   1" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.81    5.32 2.00e-01 2.50e+01 7.09e+02
  chirality model="   1" pdb=" CB  ILE A  78 "
            model="   1" pdb=" CA  ILE A  78 "
            model="   1" pdb=" CG1 ILE A  78 "
            model="   1" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.66    5.30 2.00e-01 2.50e+01 7.03e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  91 "   -0.180 2.00e-02 2.50e+03   7.03e-02 1.48e+02
        model="   1" pdb=" CG  TYR A  91 "    0.029 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  91 "    0.039 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  91 "    0.044 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  91 "    0.015 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  91 "   -0.019 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  91 "   -0.111 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  91 "    0.061 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  91 "    0.074 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  91 "    0.020 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  91 "    0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CA  GLY A  94 "   -0.061 2.00e-02 2.50e+03   1.14e-01 1.30e+02
        model="   1" pdb=" C   GLY A  94 "    0.197 2.00e-02 2.50e+03
        model="   1" pdb=" O   GLY A  94 "   -0.072 2.00e-02 2.50e+03
        model="   1" pdb=" N   ASP A  95 "   -0.065 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  12 "   -0.089 2.00e-02 2.50e+03   4.11e-02 5.08e+01
        model="   1" pdb=" CG  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  12 "   -0.085 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  12 "    0.045 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  12 "    0.040 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 188
        2.20 -     2.80: 4413
        2.80 -     3.40: 6338
        3.40 -     4.00: 7669
        4.00 -     4.60: 11710
  Nonbonded interactions: 30318
  Sorted by model distance:
  nonbonded model="   1" pdb=" HA  ILE A  78 "
            model="   1" pdb=" HA  LEU A  93 "
     model   vdw
     1.599 2.440
  nonbonded model="   1" pdb=" H   ILE A  78 "
            model="   1" pdb="HG22 ILE A  78 "
     model   vdw
     1.724 2.270
  nonbonded model="   1" pdb=" OD2 ASP A  36 "
            model="   1" pdb=" HH  TYR A  68 "
     model   vdw
     1.783 1.850
  nonbonded model="   1" pdb=" OD1 ASP A  44 "
            model="   1" pdb=" HG  SER A  46 "
     model   vdw
     1.792 1.850
  nonbonded model="   1" pdb=" H   THR A  92 "
            model="   1" pdb=" HA  LEU A  99 "
     model   vdw
     1.796 2.270
  ... (remaining 30313 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  ASP A  74 "
        model="   1" pdb=" CB  ILE A  78 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CB  THR A  92 "
        model="   1" pdb=" CB  LEU A  93 "
        model="   1" pdb=" CB  LEU A 119 "
        model="   1" pdb=" CB  ILE A 122 "
        model="   1" pdb=" CB  ALA A 124 "
        model="   1" pdb=" CB  ARG A 127 "
        model="   1" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  242

  Time building geometry restraints manager: 0.96 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  12" pdb=" CB  GLU A 120 "
        model="  12" pdb=" CB  HIS A 136 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 1.29 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 78
        1.23 -     1.43: 396
        1.43 -     1.62: 658
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   1" pdb=" N   MET A 128 "
       model="   1" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.551 -0.093 1.90e-02 2.77e+03 2.41e+01
  bond model="   1" pdb=" CA  ALA A 124 "
       model="   1" pdb=" C   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.525  1.441  0.084 2.10e-02 2.27e+03 1.62e+01
  bond model="   1" pdb=" CA  LYS A  79 "
       model="   1" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.605 -0.080 2.10e-02 2.27e+03 1.47e+01
  bond model="   1" pdb=" CA  LEU A  93 "
       model="   1" pdb=" CB  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.599 -0.069 2.00e-02 2.50e+03 1.20e+01
  bond model="   1" pdb=" N   ILE A  77 "
       model="   1" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.521 -0.063 1.90e-02 2.77e+03 1.10e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       87.92 -    97.15: 8
       97.15 -   106.38: 208
      106.38 -   115.61: 2751
      115.61 -   124.84: 990
      124.84 -   134.07: 122
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   1" pdb=" C   TYR A  89 "
        model="   1" pdb=" N   SER A  90 "
        model="   1" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  107.65   14.05 1.80e+00 3.09e-01 6.09e+01
  angle model="   1" pdb=" C   ILE A  51 "
        model="   1" pdb=" CA  ILE A  51 "
        model="   1" pdb=" CB  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     111.60  126.79  -15.19 2.00e+00 2.50e-01 5.77e+01
  angle model="   1" pdb=" CA  HIS A 135 "
        model="   1" pdb=" CB  HIS A 135 "
        model="   1" pdb=" CG  HIS A 135 "
      ideal   model   delta    sigma   weight residual
     113.80  121.14   -7.34 1.00e+00 1.00e+00 5.39e+01
  angle model="   1" pdb=" CA  VAL A 126 "
        model="   1" pdb=" CB  VAL A 126 "
        model="   1" pdb=" CG1 VAL A 126 "
      ideal   model   delta    sigma   weight residual
     110.40  122.69  -12.29 1.70e+00 3.46e-01 5.23e+01
  angle model="   1" pdb=" C   ILE A  51 "
        model="   1" pdb=" CA  ILE A  51 "
        model="   1" pdb=" HA  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   87.92   21.08 3.00e+00 1.11e-01 4.94e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.32: 896
       19.32 -    38.65: 73
       38.65 -    57.97: 26
       57.97 -    77.29: 12
       77.29 -    96.62: 4
  Dihedral angle restraints: 1011
    sinusoidal: 562
      harmonic: 449
  Sorted by residual:
  dihedral model="   1" pdb=" CA  ILE A  77 "
           model="   1" pdb=" C   ILE A  77 "
           model="   1" pdb=" N   ILE A  78 "
           model="   1" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -83.38  -96.62     0      5.00e+00 4.00e-02 3.73e+02
  dihedral model="   1" pdb=" CA  ASP A 118 "
           model="   1" pdb=" C   ASP A 118 "
           model="   1" pdb=" N   LEU A 119 "
           model="   1" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   86.05   93.95     0      5.00e+00 4.00e-02 3.53e+02
  dihedral model="   1" pdb=" CA  THR A  92 "
           model="   1" pdb=" C   THR A  92 "
           model="   1" pdb=" N   LEU A  93 "
           model="   1" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -89.61  -90.39     0      5.00e+00 4.00e-02 3.27e+02
  ... (remaining 1008 not shown)

  Histogram of chiral volume deviations from ideal:
       0.003 -    1.123: 160
       1.123 -    2.243: 0
       2.243 -    3.363: 1
       3.363 -    4.482: 2
       4.482 -    5.602: 13
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  LYS A  79 "
            model="   1" pdb=" N   LYS A  79 "
            model="   1" pdb=" C   LYS A  79 "
            model="   1" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.09    5.60 2.00e-01 2.50e+01 7.85e+02
  chirality model="   1" pdb=" CB  ILE A 131 "
            model="   1" pdb=" CA  ILE A 131 "
            model="   1" pdb=" CG1 ILE A 131 "
            model="   1" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.72    5.36 2.00e-01 2.50e+01 7.20e+02
  chirality model="   1" pdb=" CA  LEU A  93 "
            model="   1" pdb=" N   LEU A  93 "
            model="   1" pdb=" C   LEU A  93 "
            model="   1" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.76    5.27 2.00e-01 2.50e+01 6.94e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CD  ARG A 129 "   -1.122 9.50e-02 1.11e+02   3.74e-01 1.48e+02
        model="   1" pdb=" NE  ARG A 129 "    0.040 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  ARG A 129 "    0.005 2.00e-02 2.50e+03
        model="   1" pdb=" NH1 ARG A 129 "    0.003 2.00e-02 2.50e+03
        model="   1" pdb=" NH2 ARG A 129 "   -0.000 2.00e-02 2.50e+03
        model="   1" pdb="HH11 ARG A 129 "    0.026 2.00e-02 2.50e+03
        model="   1" pdb="HH12 ARG A 129 "   -0.020 2.00e-02 2.50e+03
        model="   1" pdb="HH21 ARG A 129 "    0.019 2.00e-02 2.50e+03
        model="   1" pdb="HH22 ARG A 129 "   -0.023 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CA  ARG A 127 "   -0.057 2.00e-02 2.50e+03   1.17e-01 1.38e+02
        model="   1" pdb=" C   ARG A 127 "    0.203 2.00e-02 2.50e+03
        model="   1" pdb=" O   ARG A 127 "   -0.076 2.00e-02 2.50e+03
        model="   1" pdb=" N   MET A 128 "   -0.070 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  HIS A 135 "   -0.123 2.00e-02 2.50e+03   7.28e-02 1.06e+02
        model="   1" pdb=" CG  HIS A 135 "    0.107 2.00e-02 2.50e+03
        model="   1" pdb=" ND1 HIS A 135 "    0.082 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 HIS A 135 "    0.024 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 HIS A 135 "   -0.014 2.00e-02 2.50e+03
        model="   1" pdb=" NE2 HIS A 135 "   -0.078 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 HIS A 135 "    0.034 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 HIS A 135 "   -0.032 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 168
        2.16 -     2.77: 4142
        2.77 -     3.38: 6696
        3.38 -     3.99: 8261
        3.99 -     4.60: 12375
  Nonbonded interactions: 31642
  Sorted by model distance:
  nonbonded model="   1" pdb=" HA  VAL A 126 "
            model="   1" pdb=" H   MET A 128 "
     model   vdw
     1.553 2.270
  nonbonded model="   1" pdb=" HA  LYS A  79 "
            model="   1" pdb=" HA  THR A  82 "
     model   vdw
     1.643 2.440
  nonbonded model="   1" pdb=" H   ILE A  78 "
            model="   1" pdb=" HA  LEU A  93 "
     model   vdw
     1.730 2.270
  nonbonded model="   1" pdb=" HB2 LEU A  93 "
            model="   1" pdb=" H   GLY A  94 "
     model   vdw
     1.742 2.270
  nonbonded model="   1" pdb=" OD2 ASP A  36 "
            model="   1" pdb=" HH  TYR A  68 "
     model   vdw
     1.753 1.850
  ... (remaining 31637 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A LEU   31": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   61": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 64
        1.23 -     1.42: 408
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" CZ  ARG A  58 "
       model="  12" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.26e+00
  bond model="  12" pdb=" CD2 HIS A 139 "
       model="  12" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.12e+00
  bond model="  12" pdb=" CZ  ARG A  21 "
       model="  12" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.54e+00
  bond model="  12" pdb=" CD2 HIS A 138 "
       model="  12" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.41e+00
  bond model="  12" pdb=" CD2 HIS A 134 "
       model="  12" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.16e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       94.97 -   102.81: 14
      102.81 -   110.64: 2276
      110.64 -   118.48: 856
      118.48 -   126.32: 911
      126.32 -   134.16: 22
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" C   HIS A 135 "
        model="  12" pdb=" N   HIS A 136 "
        model="  12" pdb=" CA  HIS A 136 "
      ideal   model   delta    sigma   weight residual
     121.70  134.16  -12.46 1.80e+00 3.09e-01 4.79e+01
  angle model="  12" pdb=" CA  HIS A 139 "
        model="  12" pdb=" CB  HIS A 139 "
        model="  12" pdb=" CG  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     113.80  108.37    5.43 1.00e+00 1.00e+00 2.94e+01
  angle model="  12" pdb=" C   LEU A 119 "
        model="  12" pdb=" N   GLU A 120 "
        model="  12" pdb=" CA  GLU A 120 "
      ideal   model   delta    sigma   weight residual
     121.70  131.06   -9.36 1.80e+00 3.09e-01 2.70e+01
  angle model="  12" pdb=" N   GLU A 120 "
        model="  12" pdb=" CA  GLU A 120 "
        model="  12" pdb=" C   GLU A 120 "
      ideal   model   delta    sigma   weight residual
     111.00  124.62  -13.62 2.80e+00 1.28e-01 2.37e+01
  angle model="  12" pdb=" CA  ASP A 118 "
        model="  12" pdb=" CB  ASP A 118 "
        model="  12" pdb=" CG  ASP A 118 "
      ideal   model   delta    sigma   weight residual
     112.60  107.81    4.79 1.00e+00 1.00e+00 2.29e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 929
       17.64 -    35.28: 66
       35.28 -    52.92: 24
       52.92 -    70.56: 2
       70.56 -    88.20: 8
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  12" pdb=" CA  HIS A 136 "
           model="  12" pdb=" C   HIS A 136 "
           model="  12" pdb=" N   HIS A 137 "
           model="  12" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.23   35.77     0      5.00e+00 4.00e-02 5.12e+01
  dihedral model="  12" pdb=" CA  LEU A 119 "
           model="  12" pdb=" C   LEU A 119 "
           model="  12" pdb=" N   GLU A 120 "
           model="  12" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.11  -28.89     0      5.00e+00 4.00e-02 3.34e+01
  dihedral model="  12" pdb=" C   HIS A 139 "
           model="  12" pdb=" N   HIS A 139 "
           model="  12" pdb=" CA  HIS A 139 "
           model="  12" pdb=" CB  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.86   12.26     0      2.50e+00 1.60e-01 2.41e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.973: 174
       0.973 -    1.945: 0
       1.945 -    2.916: 0
       2.916 -    3.888: 0
       3.888 -    4.860: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  HIS A 136 "
            model="  12" pdb=" N   HIS A 136 "
            model="  12" pdb=" C   HIS A 136 "
            model="  12" pdb=" CB  HIS A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.35    4.86 2.00e-01 2.50e+01 5.91e+02
  chirality model="  12" pdb=" CA  GLU A 120 "
            model="  12" pdb=" N   GLU A 120 "
            model="  12" pdb=" C   GLU A 120 "
            model="  12" pdb=" CB  GLU A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.85    4.36 2.00e-01 2.50e+01 4.76e+02
  chirality model="  12" pdb=" CA  HIS A 139 "
            model="  12" pdb=" N   HIS A 139 "
            model="  12" pdb=" C   HIS A 139 "
            model="  12" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.40e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A 111 "   -0.160 2.00e-02 2.50e+03   6.47e-02 1.25e+02
        model="  12" pdb=" CG  TYR A 111 "    0.040 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A 111 "    0.031 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A 111 "    0.040 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A 111 "   -0.117 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A 111 "    0.031 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A 111 "    0.059 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A 111 "    0.038 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  12 "   -0.102 2.00e-02 2.50e+03   5.53e-02 9.18e+01
        model="  12" pdb=" CG  TYR A  12 "   -0.026 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  12 "    0.028 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  12 "   -0.124 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  12 "    0.027 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  12 "    0.059 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  12 "    0.058 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  12 "    0.029 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  50 "   -0.118 2.00e-02 2.50e+03   5.42e-02 8.81e+01
        model="  12" pdb=" CG  TYR A  50 "    0.046 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  50 "    0.041 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  50 "    0.030 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  50 "    0.079 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  50 "    0.045 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  50 "   -0.074 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  50 "   -0.041 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 367
        2.30 -     2.87: 5003
        2.87 -     3.45: 5377
        3.45 -     4.02: 6770
        4.02 -     4.60: 9979
  Nonbonded interactions: 27496
  Sorted by model distance:
  nonbonded model="  12" pdb=" OD2 ASP A  44 "
            model="  12" pdb=" HG  SER A  46 "
     model   vdw
     1.724 1.850
  nonbonded model="  12" pdb=" OD1 ASP A  74 "
            model="  12" pdb=" HZ2 LYS A  79 "
     model   vdw
     1.751 1.850
  nonbonded model="  12" pdb=" H   TYR A  81 "
            model="  12" pdb="HD22 LEU A  93 "
     model   vdw
     1.757 2.270
  nonbonded model="  12" pdb=" OE2 GLU A  24 "
            model="  12" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.807 1.850
  nonbonded model="  12" pdb=" O   HIS A 136 "
            model="  12" pdb=" H   HIS A 138 "
     model   vdw
     1.827 1.850
  ... (remaining 27491 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

  Time building chain proxies: 1.01, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.885, 59.604, 52.749, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A VAL  112": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (51.677, 54.376, 52.839, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A LEU    2": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A LEU  132": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CB  ILE A 122 "
        model="   5" pdb=" CB  ALA A 124 "
        model="   5" pdb=" CB  LYS A 125 "
        model="   5" pdb=" CB  VAL A 126 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 51
        1.23 -     1.43: 422
        1.43 -     1.62: 658
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" N   ILE A 122 "
       model="   5" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.595 -0.137 1.90e-02 2.77e+03 5.19e+01
  bond model="   5" pdb=" CA  GLY A 121 "
       model="   5" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.638 -0.122 1.80e-02 3.09e+03 4.57e+01
  bond model="   5" pdb=" N   LYS A  79 "
       model="   5" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.570 -0.112 1.90e-02 2.77e+03 3.45e+01
  bond model="   5" pdb=" C   GLY A 121 "
       model="   5" pdb=" N   ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.329  1.398 -0.069 1.40e-02 5.10e+03 2.40e+01
  bond model="   5" pdb=" C   LYS A 125 "
       model="   5" pdb=" N   VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.329  1.263  0.066 1.40e-02 5.10e+03 2.22e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       93.82 -   102.08: 25
      102.08 -   110.35: 2196
      110.35 -   118.62: 935
      118.62 -   126.88: 892
      126.88 -   135.15: 31
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" O   LYS A 125 "
        model="   5" pdb=" C   LYS A 125 "
        model="   5" pdb=" N   VAL A 126 "
      ideal   model   delta    sigma   weight residual
     123.00  103.94   19.06 1.60e+00 3.91e-01 1.42e+02
  angle model="   5" pdb=" C   ILE A 122 "
        model="   5" pdb=" N   GLU A 123 "
        model="   5" pdb=" CA  GLU A 123 "
      ideal   model   delta    sigma   weight residual
     121.70  135.15  -13.45 1.80e+00 3.09e-01 5.58e+01
  angle model="   5" pdb=" CA  HIS A 139 "
        model="   5" pdb=" CB  HIS A 139 "
        model="   5" pdb=" CG  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     113.80  120.63   -6.83 1.00e+00 1.00e+00 4.67e+01
  angle model="   5" pdb=" C   SER A  76 "
        model="   5" pdb=" N   ILE A  77 "
        model="   5" pdb=" CA  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     121.70  133.46  -11.76 1.80e+00 3.09e-01 4.27e+01
  angle model="   5" pdb=" C   ILE A  51 "
        model="   5" pdb=" CA  ILE A  51 "
        model="   5" pdb=" CB  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     111.60  124.54  -12.94 2.00e+00 2.50e-01 4.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.16: 938
       20.16 -    40.33: 50
       40.33 -    60.49: 24
       60.49 -    80.65: 5
       80.65 -   100.82: 4
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   5" pdb=" CA  LYS A 125 "
           model="   5" pdb=" C   LYS A 125 "
           model="   5" pdb=" N   VAL A 126 "
           model="   5" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   79.18  100.82     0      5.00e+00 4.00e-02 4.07e+02
  dihedral model="   5" pdb=" CA  ALA A 124 "
           model="   5" pdb=" C   ALA A 124 "
           model="   5" pdb=" N   LYS A 125 "
           model="   5" pdb=" CA  LYS A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -83.66  -96.34     0      5.00e+00 4.00e-02 3.71e+02
  dihedral model="   5" pdb=" CA  ILE A 122 "
           model="   5" pdb=" C   ILE A 122 "
           model="   5" pdb=" N   GLU A 123 "
           model="   5" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   97.31   82.69     0      5.00e+00 4.00e-02 2.73e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.149: 169
       1.149 -    2.298: 0
       2.298 -    3.446: 0
       3.446 -    4.594: 1
       4.594 -    5.743: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CA  LYS A  79 "
            model="   5" pdb=" N   LYS A  79 "
            model="   5" pdb=" C   LYS A  79 "
            model="   5" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.23    5.74 2.00e-01 2.50e+01 8.24e+02
  chirality model="   5" pdb=" CA  LYS A 125 "
            model="   5" pdb=" N   LYS A 125 "
            model="   5" pdb=" C   LYS A 125 "
            model="   5" pdb=" CB  LYS A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.98    5.50 2.00e-01 2.50e+01 7.55e+02
  chirality model="   5" pdb=" CA  ILE A 122 "
            model="   5" pdb=" N   ILE A 122 "
            model="   5" pdb=" C   ILE A 122 "
            model="   5" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -2.75    5.19 2.00e-01 2.50e+01 6.72e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  91 "   -0.605 2.00e-02 2.50e+03   2.66e-01 2.13e+03
        model="   5" pdb=" CG  TYR A  91 "    0.085 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  91 "    0.070 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  91 "    0.190 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  91 "    0.126 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  91 "   -0.085 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  91 "   -0.422 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  91 "    0.022 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  91 "    0.378 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  91 "    0.298 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  91 "   -0.061 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  50 "    0.222 2.00e-02 2.50e+03   9.67e-02 2.81e+02
        model="   5" pdb=" CG  TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  50 "   -0.045 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  50 "   -0.046 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  50 "   -0.034 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  50 "   -0.034 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  50 "    0.199 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  50 "   -0.071 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  50 "   -0.074 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  50 "   -0.055 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  50 "   -0.054 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  12 "   -0.128 2.00e-02 2.50e+03   5.72e-02 9.81e+01
        model="   5" pdb=" CG  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  12 "    0.025 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  12 "    0.026 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  12 "   -0.119 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  12 "    0.043 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  12 "    0.044 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  12 "    0.037 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  12 "    0.036 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 466
        2.32 -     2.89: 5152
        2.89 -     3.46: 5686
        3.46 -     4.03: 7306
        4.03 -     4.60: 10786
  Nonbonded interactions: 29396
  Sorted by model distance:
  nonbonded model="   5" pdb=" H   ASP A  95 "
            model="   5" pdb=" H   GLY A  96 "
     model   vdw
     1.748 2.100
  nonbonded model="   5" pdb=" OD2 ASP A  44 "
            model="   5" pdb=" HG  SER A  46 "
     model   vdw
     1.750 1.850
  nonbonded model="   5" pdb=" HB3 LYS A  85 "
            model="   5" pdb=" H   TYR A  91 "
     model   vdw
     1.756 2.270
  nonbonded model="   5" pdb=" H   LEU A  93 "
            model="   5" pdb=" HB2 LEU A  93 "
     model   vdw
     1.792 2.270
  nonbonded model="   5" pdb=" OD1 ASP A  74 "
            model="   5" pdb=" HG  SER A  76 "
     model   vdw
     1.817 1.850
  ... (remaining 29391 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A LEU    2": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.954, 70.869, 41.208, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.901, 49.82, 32.309, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.25
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  ASP A  74 "
        model="   1" pdb=" CB  ILE A  77 "
        model="   1" pdb=" CB  ILE A  78 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CB  THR A  92 "
        model="   1" pdb=" CB  ILE A 108 "
        model="   1" pdb=" CB  ASP A 118 "
        model="   1" pdb=" CB  LEU A 132 "
  Number of C-beta restraints generated:  246

  Time building geometry restraints manager: 1.26 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 64
        1.23 -     1.43: 408
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   1" pdb=" CA  ILE A  77 "
       model="   1" pdb=" C   ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.525  1.451  0.074 2.10e-02 2.27e+03 1.23e+01
  bond model="   1" pdb=" C   THR A  92 "
       model="   1" pdb=" N   LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.289  0.040 1.40e-02 5.10e+03 8.04e+00
  bond model="   1" pdb=" CD2 HIS A 139 "
       model="   1" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.78e+00
  bond model="   1" pdb=" CD2 HIS A 134 "
       model="   1" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.47e+00
  bond model="   1" pdb=" CD2 HIS A 135 "
       model="   1" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.40e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       85.47 -    95.54: 10
       95.54 -   105.61: 128
      105.61 -   115.69: 2836
      115.69 -   125.76: 1039
      125.76 -   135.84: 66
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   1" pdb=" N   SER A  97 "
        model="   1" pdb=" CA  SER A  97 "
        model="   1" pdb=" HA  SER A  97 "
      ideal   model   delta    sigma   weight residual
     110.00   85.47   24.53 3.00e+00 1.11e-01 6.69e+01
  angle model="   1" pdb=" C   TYR A  89 "
        model="   1" pdb=" N   SER A  90 "
        model="   1" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  135.84  -14.14 1.80e+00 3.09e-01 6.17e+01
  angle model="   1" pdb=" N   ILE A  86 "
        model="   1" pdb=" CA  ILE A  86 "
        model="   1" pdb=" HA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     110.00   88.76   21.24 3.00e+00 1.11e-01 5.01e+01
  angle model="   1" pdb=" C   SER A  97 "
        model="   1" pdb=" CA  SER A  97 "
        model="   1" pdb=" HA  SER A  97 "
      ideal   model   delta    sigma   weight residual
     109.00   87.84   21.16 3.00e+00 1.11e-01 4.98e+01
  angle model="   1" pdb=" CA  ILE A  86 "
        model="   1" pdb=" CB  ILE A  86 "
        model="   1" pdb=" CG1 ILE A  86 "
      ideal   model   delta    sigma   weight residual
     110.40  121.41  -11.01 1.70e+00 3.46e-01 4.19e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 902
       17.37 -    34.74: 79
       34.74 -    52.11: 23
       52.11 -    69.49: 8
       69.49 -    86.86: 3
  Dihedral angle restraints: 1015
    sinusoidal: 562
      harmonic: 453
  Sorted by residual:
  dihedral model="   1" pdb=" C   SER A  97 "
           model="   1" pdb=" N   SER A  97 "
           model="   1" pdb=" CA  SER A  97 "
           model="   1" pdb=" CB  SER A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -163.80   41.20     0      2.50e+00 1.60e-01 2.72e+02
  dihedral model="   1" pdb=" N   SER A  97 "
           model="   1" pdb=" C   SER A  97 "
           model="   1" pdb=" CA  SER A  97 "
           model="   1" pdb=" CB  SER A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  163.90  -41.10     0      2.50e+00 1.60e-01 2.70e+02
  dihedral model="   1" pdb=" CA  LYS A  79 "
           model="   1" pdb=" C   LYS A  79 "
           model="   1" pdb=" N   GLY A  80 "
           model="   1" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -110.73  -69.27     0      5.00e+00 4.00e-02 1.92e+02
  ... (remaining 1012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.062: 164
       1.062 -    2.124: 2
       2.124 -    3.186: 0
       3.186 -    4.248: 3
       4.248 -    5.309: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  THR A  92 "
            model="   1" pdb=" N   THR A  92 "
            model="   1" pdb=" C   THR A  92 "
            model="   1" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.78    5.31 2.00e-01 2.50e+01 7.05e+02
  chirality model="   1" pdb=" CB  ILE A  78 "
            model="   1" pdb=" CA  ILE A  78 "
            model="   1" pdb=" CG1 ILE A  78 "
            model="   1" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.64    5.28 2.00e-01 2.50e+01 6.98e+02
  chirality model="   1" pdb=" CA  LYS A  79 "
            model="   1" pdb=" N   LYS A  79 "
            model="   1" pdb=" C   LYS A  79 "
            model="   1" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.71    5.22 2.00e-01 2.50e+01 6.82e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  PHE A  15 "   -0.277 2.00e-02 2.50e+03   1.16e-01 4.06e+02
        model="   1" pdb=" CG  PHE A  15 "    0.038 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 PHE A  15 "    0.087 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 PHE A  15 "    0.047 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 PHE A  15 "   -0.007 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 PHE A  15 "    0.032 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  PHE A  15 "   -0.060 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 PHE A  15 "    0.182 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 PHE A  15 "    0.064 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 PHE A  15 "   -0.033 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 PHE A  15 "    0.083 2.00e-02 2.50e+03
        model="   1" pdb=" HZ  PHE A  15 "   -0.156 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  12 "    0.157 2.00e-02 2.50e+03   7.29e-02 1.59e+02
        model="   1" pdb=" CG  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  12 "   -0.033 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  12 "   -0.029 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  12 "   -0.026 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  12 "   -0.031 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  12 "    0.160 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  12 "   -0.055 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  12 "   -0.043 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  12 "   -0.041 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  12 "   -0.055 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  91 "   -0.085 2.00e-02 2.50e+03   5.30e-02 8.43e+01
        model="   1" pdb=" CG  TYR A  91 "   -0.016 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  91 "    0.041 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  91 "   -0.023 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  91 "    0.019 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  91 "   -0.014 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  91 "   -0.023 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  91 "    0.122 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  91 "   -0.071 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  91 "    0.054 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 255
        2.25 -     2.84: 4814
        2.84 -     3.42: 6247
        3.42 -     4.01: 7796
        4.01 -     4.60: 11611
  Nonbonded interactions: 30723
  Sorted by model distance:
  nonbonded model="   1" pdb=" HB  THR A  92 "
            model="   1" pdb=" HA  LEU A  93 "
     model   vdw
     1.662 2.440
  nonbonded model="   1" pdb=" HA  THR A  92 "
            model="   1" pdb="HD23 LEU A  93 "
     model   vdw
     1.736 2.440
  nonbonded model="   1" pdb=" H   LYS A  79 "
            model="   1" pdb="HD22 LEU A  93 "
     model   vdw
     1.776 2.270
  nonbonded model="   1" pdb="HG13 ILE A  86 "
            model="   1" pdb=" H   SER A  90 "
     model   vdw
     1.831 2.270
  nonbonded model="   1" pdb=" O   VAL A 126 "
            model="   1" pdb=" HG  SER A 130 "
     model   vdw
     1.842 1.850
  ... (remaining 30718 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 130}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (58.393, 38.451, 50.034, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.50e+00
  bond model="   9" pdb=" CZ  ARG A 127 "
       model="   9" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.326  0.004 1.30e-02 5.92e+03 8.17e-02
  bond model="   9" pdb=" NE  ARG A  21 "
       model="   9" pdb=" CZ  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 8.12e-02
  bond model="   9" pdb=" CZ  ARG A  21 "
       model="   9" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.326  0.004 1.30e-02 5.92e+03 7.39e-02
  bond model="   9" pdb=" CZ  ARG A  58 "
       model="   9" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.327 -0.004 1.40e-02 5.10e+03 7.04e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.89 -   106.89: 64
      106.89 -   112.89: 2721
      112.89 -   118.89: 426
      118.89 -   124.89: 824
      124.89 -   130.89: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A 117 "
        model="   9" pdb=" CA  PRO A 117 "
        model="   9" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   9" pdb=" CB  PRO A 114 "
        model="   9" pdb=" CA  PRO A 114 "
        model="   9" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   9" pdb=" CB  PRO A  52 "
        model="   9" pdb=" CA  PRO A  52 "
        model="   9" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   9" pdb=" CB  PRO A 102 "
        model="   9" pdb=" CA  PRO A 102 "
        model="   9" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A   6 "
        model="   9" pdb=" CA  PRO A   6 "
        model="   9" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 861
       16.62 -    33.24: 88
       33.24 -    49.86: 52
       49.86 -    66.48: 26
       66.48 -    83.11: 5
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CA  ASP A  44 "
           model="   9" pdb=" CB  ASP A  44 "
           model="   9" pdb=" CG  ASP A  44 "
           model="   9" pdb=" OD1 ASP A  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.48   59.48     1      2.00e+01 2.50e-03 1.18e+01
  dihedral model="   9" pdb=" N   GLU A  32 "
           model="   9" pdb=" CA  GLU A  32 "
           model="   9" pdb=" CB  GLU A  32 "
           model="   9" pdb=" CG  GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -120.62  -59.38     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   9" pdb=" CA  ILE A  86 "
           model="   9" pdb=" CB  ILE A  86 "
           model="   9" pdb=" CG1 ILE A  86 "
           model="   9" pdb=" CD1 ILE A  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.27   58.73     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.020: 104
       0.020 -    0.039: 49
       0.039 -    0.058: 4
       0.058 -    0.077: 0
       0.077 -    0.096: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A   4 "
            model="   9" pdb=" N   ILE A   4 "
            model="   9" pdb=" C   ILE A   4 "
            model="   9" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.31e-01
  chirality model="   9" pdb=" CA  ILE A  30 "
            model="   9" pdb=" N   ILE A  30 "
            model="   9" pdb=" C   ILE A  30 "
            model="   9" pdb=" CB  ILE A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.30e-01
  chirality model="   9" pdb=" CA  ILE A  37 "
            model="   9" pdb=" N   ILE A  37 "
            model="   9" pdb=" C   ILE A  37 "
            model="   9" pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.27e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  15 "    0.001 2.00e-02 2.50e+03   1.30e-03 5.09e-02
        model="   9" pdb=" CG  PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  15 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  15 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  45 "   -0.000 2.00e-02 2.50e+03   1.30e-03 5.04e-02
        model="   9" pdb=" CG  PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  45 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  45 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  45 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  68 "    0.001 2.00e-02 2.50e+03   1.15e-03 3.99e-02
        model="   9" pdb=" CG  TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  68 "    0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 262
        2.22 -     2.81: 478        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}
8
        2.81 -     3.41: 5666
        3.41 -     4.00: 7158
        4.00 -     4.60: 10678
  Nonbonded interactions: 28552
  Sorted by model distance:
  nonbonded model="   9" pdb="HD13 LEU A   3 "
            model="   9" pdb="HG21 ILE A  51 "
     model   vdw
     1.620 2.440
  nonbonded model="   9" pdb="HD23 LEU A   9 "
            model="   9" pdb="HD22 LEU A  26 "
     model   vdw
     1.709 2.440
  nonbonded model="   9" pdb="HG23 ILE A  37 "
            model="   9" pdb="HG21 ILE A 108 "
     model   vdw
     1.742 2.440
  nonbonded model="   9" pdb=" HD3 LYS A  40 "
            model="   9" pdb="HD11 ILE A 108 "
     model   vdw
     1.773 2.440
  nonbonded model="   9" pdb="HD12 ILE A  37 "
            model="   9" pdb="HD23 LEU A  61 "
     model   vdw
     1.775 2.440
  ... (remaining 28547 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 129}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 128}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (46.87, 39.756, 47.248, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 0.99, per 1000 atoms: 0.45
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (66.443, 49.393, 76.309, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.355, 57.747, 55.826, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (78.098, 43.503, 58.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.505, 52.031, 46.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.25, per 1000 atoms: 0.56
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (58.389, 46.42, 50.984, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 0.81, per 1000 atoms: 0.37
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.406, 46.928, 43.612, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  13" pdb=" CB  ASP A  88 "
        model="  13" pdb=" CB  TYR A  89 "
        model="  13" pdb=" CB  LEU A  99 "
        model="  13" pdb=" CB  LEU A 132 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 0.98 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   61": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A LEU  119": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.528, 53.188, 98.339, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (43.809, 47.157, 58.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 97
        1.23 -     1.43: 375
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" CZ  ARG A  58 "
       model="  13" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.14e+00
  bond model="  13" pdb=" CD2 HIS A 139 "
       model="  13" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.71e+00
  bond model="  13" pdb=" CE1 HIS A 139 "
       model="  13" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.08e+00
  bond model="  13" pdb=" CD2 HIS A 134 "
       model="  13" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.93e+00
  bond model="  13" pdb=" CD2 HIS A 137 "
       model="  13" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.78e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       92.35 -   101.13: 9
      101.13 -   109.91: 2054
      109.91 -   118.68: 1107
      118.68 -   127.46: 896
      127.46 -   136.24: 13
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" C   ILE A 131 "
        model="  13" pdb=" N   LEU A 132 "
        model="  13" pdb=" CA  LEU A 132 "
      ideal   model   delta    sigma   weight residual
     121.70  136.24  -14.54 1.80e+00 3.09e-01 6.52e+01
  angle model="  13" pdb=" C   ASP A  88 "
        model="  13" pdb=" N   TYR A  89 "
        model="  13" pdb=" CA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     121.70  109.96   11.74 1.80e+00 3.09e-01 4.25e+01
  angle model="  13" pdb=" C   LEU A  99 "
        model="  13" pdb=" CA  LEU A  99 "
        model="  13" pdb=" CB  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     110.10  120.72  -10.62 1.90e+00 2.77e-01 3.13e+01
  angle model="  13" pdb=" CB  LEU A  99 "
        model="  13" pdb=" CA  LEU A  99 "
        model="  13" pdb=" HA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     109.00   92.35   16.65 3.00e+00 1.11e-01 3.08e+01
  angle model="  13" pdb=" C   TYR A  89 "
        model="  13" pdb=" CA  TYR A  89 "
        model="  13" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   93.21   15.79 3.00e+00 1.11e-01 2.77e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.49: 941
       18.49 -    36.98: 54
       36.98 -    55.47: 17
       55.47 -    73.96: 7
       73.96 -    92.45: 6
  Dihedral angle restraints: 1025
    sinusoidal: 562
      harmonic: 463
  Sorted by residual:
  dihedral model="  13" pdb=" CA  ASP A  88 "
           model="  13" pdb=" C   ASP A  88 "
           model="  13" pdb=" N   TYR A  89 "
           model="  13" pdb=" CA  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  117.28   62.72     0      5.00e+00 4.00e-02 1.57e+02
  dihedral model="  13" pdb=" CA  TYR A  89 "
           model="  13" pdb=" C   TYR A  89 "
           model="  13" pdb=" N   SER A  90 "
           model="  13" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.65   45.35     0      5.00e+00 4.00e-02 8.23e+01
  dihedral model="  13" pdb=" CA  LEU A 132 "
           model="  13" pdb=" C   LEU A 132 "
           model="  13" pdb=" N   GLU A 133 "
           model="  13" pdb=" CA  GLU A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.06   33.94     0      5.00e+00 4.00e-02 4.61e+01
  ... (remaining 1022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.922: 172
       0.922 -    1.842: 0
       1.842 -    2.762: 0
       2.762 -    3.682: 1
       3.682 -    4.603: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  ASP A  88 "
            model="  13" pdb=" N   ASP A  88 "
            model="  13" pdb=" C   ASP A  88 "
            model="  13" pdb=" CB  ASP A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.09    4.60 2.00e-01 2.50e+01 5.30e+02
  chirality model="  13" pdb=" CA  TYR A  89 "
            model="  13" pdb=" N   TYR A  89 "
            model="  13" pdb=" C   TYR A  89 "
            model="  13" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.66    4.17 2.00e-01 2.50e+01 4.35e+02
  chirality model="  13" pdb=" CA  LEU A 132 "
            model="  13" pdb=" N   LEU A 132 "
            model="  13" pdb=" C   LEU A 132 "
            model="  13" pdb=" CB  LEU A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.55    4.06 2.00e-01 2.50e+01 4.12e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  50 "    0.202 2.00e-02 2.50e+03   1.00e-01 3.02e+02
        model="  13" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  50 "   -0.032 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  50 "   -0.044 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  50 "   -0.050 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  50 "   -0.039 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  50 "    0.233 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  50 "   -0.045 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  50 "   -0.081 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  50 "   -0.081 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  50 "   -0.048 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  PHE A  67 "    0.198 2.00e-02 2.50e+03   8.14e-02 1.99e+02
        model="  13" pdb=" CG  PHE A  67 "   -0.030 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 PHE A  67 "   -0.039 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 PHE A  67 "   -0.056 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 PHE A  67 "   -0.020 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 PHE A  67 "   -0.003 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  PHE A  67 "    0.045 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 PHE A  67 "   -0.057 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 PHE A  67 "   -0.108 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 PHE A  67 "   -0.051 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="  13" pdb=" HZ  PHE A  67 "    0.122 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  PHE A  15 "    0.174 2.00e-02 2.50e+03   7.54e-02 1.71e+02
        model="  13" pdb=" CG  PHE A  15 "   -0.012 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 PHE A  15 "   -0.030 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 PHE A  15 "   -0.052 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 PHE A  15 "   -0.024 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  PHE A  15 "    0.042 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 PHE A  15 "   -0.045 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 PHE A  15 "   -0.113 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 PHE A  15 "   -0.063 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 PHE A  15 "    0.008 2.00e-02 2.50e+03
        model="  13" pdb=" HZ  PHE A  15 "    0.114 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 217
        2.23 -     2.83: 4627
        2.83 -     3.42: 5940
        3.42 -     4.01: 7365
        4.01 -     4.60: 11107
  Nonbonded interactions: 29256
  Sorted by model distance:
  nonbonded model="  13" pdb=" HA  SER A  13 "
            model="  13" pdb="HE21 GLN A  66 "
     model   vdw
     1.643 2.270
  nonbonded model="  13" pdb=" HA  ILE A 131 "
            model="  13" pdb=" H   LEU A 132 "
     model   vdw
     1.763 2.270
  nonbonded model="  13" pdb=" H   VAL A  14 "
            model="  13" pdb="HG22 VAL A  14 "
     model   vdw
     1.800 2.270
  nonbonded model="  13" pdb=" OD2 ASP A  44 "
            model="  13" pdb=" HG  SER A  46 "
     model   vdw
     1.803 1.850
  nonbonded model="  13" pdb=" OD2 ASP A  36 "
            model="  13" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.804 1.850
  ... (remaining 29251 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   8" pdb=" N   MET A   1 "
       model="   8" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.45e+00
  bond model="   8" pdb=" CZ  ARG A 129 "
       model="   8" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 7.22e-02
  bond model="   8" pdb=" NE  ARG A 129 "
       model="   8" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 5.76e-02
  bond model="   8" pdb=" NE  ARG A 127 "
       model="   8" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 5.55e-02
  bond model="   8" pdb=" CZ  ARG A  21 "
       model="   8" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.05e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.87 -   106.88: 64
      106.88 -   112.88: 2721
      112.88 -   118.89: 426
      118.89 -   124.90: 824
      124.90 -   130.91: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   8" pdb=" CB  PRO A   6 "
        model="   8" pdb=" CA  PRO A   6 "
        model="   8" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.60e+00
  angle model="   8" pdb=" CB  PRO A  22 "
        model="   8" pdb=" CA  PRO A  22 "
        model="   8" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   8" pdb=" CB  PRO A 117 "
        model="   8" pdb=" CA  PRO A 117 "
        model="   8" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   8" pdb=" CB  PRO A 102 "
        model="   8" pdb=" CA  PRO A 102 "
        model="   8" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  angle model="   8" pdb=" CB  PRO A  52 "
        model="   8" pdb=" CA  PRO A  52 "
        model="   8" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.76   -4.76 3.00e+00 1.11e-01 2.52e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 877
       17.78 -    35.57: 83
       35.57 -    53.35: 44
       53.35 -    71.13: 25
       71.13 -    88.92: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   8" pdb=" CB  GLU A  55 "
           model="   8" pdb=" CG  GLU A  55 "
           model="   8" pdb=" CD  GLU A  55 "
           model="   8" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.92   88.92     1      3.00e+01 1.11e-03 1.05e+01
  dihedral model="   8" pdb=" CA  ASP A  29 "
           model="   8" pdb=" CB  ASP A  29 "
           model="   8" pdb=" CG  ASP A  29 "
           model="   8" pdb=" OD1 ASP A  29 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.68   54.68     1      2.00e+01 2.50e-03 1.01e+01
  dihedral model="   8" pdb=" CB  GLU A  24 "
           model="   8" pdb=" CG  GLU A  24 "
           model="   8" pdb=" CD  GLU A  24 "
           model="   8" pdb=" OE1 GLU A  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.67   83.67     1      3.00e+01 1.11e-03 9.49e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 101
       0.019 -    0.038: 50
       0.038 -    0.057: 6
       0.057 -    0.076: 0
       0.076 -    0.095: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  ILE A 108 "
            model="   8" pdb=" N   ILE A 108 "
            model="   8" pdb=" C   ILE A 108 "
            model="   8" pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.24e-01
  chirality model="   8" pdb=" CA  ILE A  38 "
            model="   8" pdb=" N   ILE A  38 "
            model="   8" pdb=" C   ILE A  38 "
            model="   8" pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.18e-01
  chirality model="   8" pdb=" CA  ILE A  86 "
            model="   8" pdb=" N   ILE A  86 "
            model="   8" pdb=" C   ILE A  86 "
            model="   8" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.17e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  68 "    0.000 2.00e-02 2.50e+03   1.60e-03 7.71e-02
        model="   8" pdb=" CG  TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  68 "   -0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  68 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  68 "    0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  68 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  12 "   -0.000 2.00e-02 2.50e+03   1.14e-03 3.90e-02
        model="   8" pdb=" CG  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  PHE A  15 "    0.001 2.00e-02 2.50e+03   1.06e-03 3.38e-02
        model="   8" pdb=" CG  PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 PHE A  15 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 PHE A  15 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HZ  PHE A  15 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.32 -     1.98: 30
        1.98 -     2.63: 2962
        2.63 -     3.29: 6527
        3.29 -     3.94: 7409
        3.94 -     4.60: 11251
  Nonbonded interactions: 28179
  Sorted by model distance:
  nonbonded model="   8" pdb="HD11 LEU A  93 "
            model="   8" pdb="HD13 LEU A  99 "
     model   vdw
     1.319 2.440
  nonbonded model="   8" pdb="HD23 LEU A   9 "
            model="   8" pdb="HD22 LEU A  26 "
     model   vdw
     1.541 2.440
  nonbonded model="   8" pdb="HG23 ILE A  37 "
            model="   8" pdb="HD13 ILE A 108 "
     model   vdw
     1.611 2.440
  nonbonded model="   8" pdb="HG12 VAL A  41 "
            model="   8" pdb=" HA  VAL A 112 "
     model   vdw
     1.744 2.440
  nonbonded model="   8" pdb=" HG2 PRO A 117 "
            model="   8" pdb="HD23 LEU A 119 "
     model   vdw
     1.757 2.440
  ... (remaining 28174 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   70": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (67.511, 50.853, 52.007, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.989, 54.919, 59.506, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.71, 78.974, 71.179, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  13" pdb=" CB  LEU A  99 "
  Number of C-beta restraints generated:  262

  Time building geometry restraints manager: 1.08 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  SER A  97 "
        model="   5" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  258

  Time building geometry restraints manager: 0.71 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 71
        1.23 -     1.42: 402
        1.42 -     1.62: 659
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" CD2 HIS A 139 "
       model="  13" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.69e+00
  bond model="  13" pdb=" CZ  ARG A  21 "
       model="  13" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.48e+00
  bond model="  13" pdb=" CD2 HIS A  43 "
       model="  13" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.37e+00
  bond model="  13" pdb=" CD2 HIS A 138 "
       model="  13" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.08e+00
  bond model="  13" pdb=" CZ  ARG A 129 "
       model="  13" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.70e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.63 -   106.69: 198
      106.69 -   113.75: 2641
      113.75 -   120.80: 732
      120.80 -   127.86: 499
      127.86 -   134.91: 9
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" C   SER A  98 "
        model="  13" pdb=" N   LEU A  99 "
        model="  13" pdb=" CA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     121.70  134.91  -13.21 1.80e+00 3.09e-01 5.39e+01
  angle model="  13" pdb=" CA  PHE A  45 "
        model="  13" pdb=" CB  PHE A  45 "
        model="  13" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  120.15   -6.35 1.00e+00 1.00e+00 4.04e+01
  angle model="  13" pdb=" CA  SER A  98 "
        model="  13" pdb=" C   SER A  98 "
        model="  13" pdb=" N   LEU A  99 "
      ideal   model   delta    sigma   weight residual
     116.20  105.11   11.09 2.00e+00 2.50e-01 3.08e+01
  angle model="  13" pdb=" OE1 GLN A 100 "
        model="  13" pdb=" CD  GLN A 100 "
        model="  13" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.29    4.31 1.00e+00 1.00e+00 1.86e+01
  angle model="  13" pdb=" OE1 GLN A  28 "
        model="  13" pdb=" CD  GLN A  28 "
        model="  13" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.45    4.15 1.00e+00 1.00e+00 1.73e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 943
       17.65 -    35.31: 53
       35.31 -    52.96: 20
       52.96 -    70.62: 9
       70.62 -    88.27: 6
  Dihedral angle restraints: 1031
    sinusoidal: 562
      harmonic: 469
  Sorted by residual:
  dihedral model="  13" pdb=" CA  SER A  46 "
           model="  13" pdb=" C   SER A  46 "
           model="  13" pdb=" N   ASP A  47 "
           model="  13" pdb=" CA  ASP A  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.30  -38.70     0      5.00e+00 4.00e-02 5.99e+01
  dihedral model="  13" pdb=" C   GLN A 100 "
           model="  13" pdb=" N   GLN A 100 "
           model="  13" pdb=" CA  GLN A 100 "
           model="  13" pdb=" CB  GLN A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.34    9.74     0      2.50e+00 1.60e-01 1.52e+01
  dihedral model="  13" pdb=" CA  PRO A 114 "
           model="  13" pdb=" C   PRO A 114 "
           model="  13" pdb=" N   ALA A 115 "
           model="  13" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 1028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.897: 175
       0.897 -    1.793: 0
       1.793 -    2.690: 0
       2.690 -    3.586: 0
       3.586 -    4.482: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  LEU A  99 "
            model="  13" pdb=" N   LEU A  99 "
            model="  13" pdb=" C   LEU A  99 "
            model="  13" pdb=" CB  LEU A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.97    4.48 2.00e-01 2.50e+01 5.02e+02
  chirality model="  13" pdb=" CA  SER A  98 "
            model="  13" pdb=" N   SER A  98 "
            model="  13" pdb=" C   SER A  98 "
            model="  13" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.20e+00
  chirality model="  13" pdb=" CA  LEU A 132 "
            model="  13" pdb=" N   LEU A 132 "
            model="  13" pdb=" C   LEU A 132 "
            model="  13" pdb=" CB  LEU A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  50 "   -0.247 2.00e-02 2.50e+03   1.14e-01 3.91e+02
        model="  13" pdb=" CG  TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  50 "    0.038 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  50 "    0.060 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  50 "    0.051 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  50 "    0.029 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  50 "   -0.235 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  50 "    0.062 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  50 "    0.129 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  50 "    0.100 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  50 "    0.034 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  81 "   -0.084 2.00e-02 2.50e+03   8.02e-02 1.93e+02
        model="  13" pdb=" CG  TYR A  81 "    0.041 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  81 "   -0.017 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  81 "    0.060 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  81 "    0.050 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  81 "    0.061 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  81 "   -0.058 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  81 "   -0.100 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  81 "    0.129 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  81 "    0.085 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  81 "   -0.143 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A 111 "    0.190 2.00e-02 2.50e+03   7.28e-02 1.59e+02
        model="  13" pdb=" CG  TYR A 111 "   -0.034 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A 111 "   -0.043 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A 111 "   -0.045 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A 111 "    0.104 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A 111 "   -0.071 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A 111 "   -0.074 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A 111 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.34: 522
        2.34 -     2.90: 5037
        2.90 -     3.47: 5474
        3.47 -     4.03: 7094
        4.03 -     4.60: 10407
  Nonbonded interactions: 28534
  Sorted by model distance:
  nonbonded model="  13" pdb=" HZ2 LYS A  85 "
            model="  13" pdb=" OD1 ASP A  88 "
     model   vdw
     1.774 1.850
  nonbonded model="  13" pdb="HG22 ILE A  71 "
            model="  13" pdb="HG21 ILE A  77 "
     model   vdw
     1.811 2.440
  nonbonded model="  13" pdb=" OE2 GLU A  24 "
            model="  13" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.815 1.850
  nonbonded model="  13" pdb=" HZ3 LYS A  10 "
            model="  13" pdb=" OD1 ASP A  23 "
     model   vdw
     1.816 1.850
  nonbonded model="  13" pdb=" OE1 GLU A  16 "
            model="  13" pdb=" HZ1 LYS A  19 "
     model   vdw
     1.850 1.850
  ... (remaining 28529 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 70
        1.23 -     1.43: 406
        1.43 -     1.62: 656
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" N   GLY A  80 "
       model="   5" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.544 -0.093 1.60e-02 3.91e+03 3.35e+01
  bond model="   5" pdb=" N   LYS A  79 "
       model="   5" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.350  0.108 1.90e-02 2.77e+03 3.20e+01
  bond model="   5" pdb=" CA  LYS A  79 "
       model="   5" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.614 -0.089 2.10e-02 2.27e+03 1.81e+01
  bond model="   5" pdb=" N   ILE A  78 "
       model="   5" pdb=" CA  ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.458  1.391  0.067 1.90e-02 2.77e+03 1.24e+01
  bond model="   5" pdb=" C   ILE A  78 "
       model="   5" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.280  0.049 1.40e-02 5.10e+03 1.22e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       55.98 -    77.40: 1
       77.40 -    98.83: 7
       98.83 -   120.25: 3470
      120.25 -   141.68: 600
      141.68 -   163.10: 1
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" CB  TYR A  89 "
        model="   5" pdb=" CA  TYR A  89 "
        model="   5" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00  163.10  -54.10 3.00e+00 1.11e-01 3.25e+02
  angle model="   5" pdb=" N   TYR A  89 "
        model="   5" pdb=" CA  TYR A  89 "
        model="   5" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.00   55.98   54.02 3.00e+00 1.11e-01 3.24e+02
  angle model="   5" pdb=" N   TYR A  89 "
        model="   5" pdb=" CA  TYR A  89 "
        model="   5" pdb=" C   TYR A  89 "
      ideal   model   delta    sigma   weight residual
     111.00  136.11  -25.11 2.80e+00 1.28e-01 8.04e+01
  angle model="   5" pdb=" C   TYR A  89 "
        model="   5" pdb=" CA  TYR A  89 "
        model="   5" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   82.58   26.42 3.00e+00 1.11e-01 7.75e+01
  angle model="   5" pdb=" C   GLY A  80 "
        model="   5" pdb=" N   TYR A  81 "
        model="   5" pdb=" CA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     121.70  137.14  -15.44 1.80e+00 3.09e-01 7.35e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.39: 958
       22.39 -    44.78: 45
       44.78 -    67.17: 19
       67.17 -    89.56: 4
       89.56 -   111.95: 1
  Dihedral angle restraints: 1027
    sinusoidal: 562
      harmonic: 465
  Sorted by residual:
  dihedral model="   5" pdb=" CA  TYR A  89 "
           model="   5" pdb=" C   TYR A  89 "
           model="   5" pdb=" N   SER A  90 "
           model="   5" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -68.05 -111.95     0      5.00e+00 4.00e-02 5.01e+02
  dihedral model="   5" pdb=" N   TYR A  89 "
           model="   5" pdb=" C   TYR A  89 "
           model="   5" pdb=" CA  TYR A  89 "
           model="   5" pdb=" CB  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  174.94  -52.14     0      2.50e+00 1.60e-01 4.35e+02
  dihedral model="   5" pdb=" C   TYR A  89 "
           model="   5" pdb=" N   TYR A  89 "
           model="   5" pdb=" CA  TYR A  89 "
           model="   5" pdb=" CB  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -174.68   52.08     0      2.50e+00 1.60e-01 4.34e+02
  ... (remaining 1024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.009: 171
       1.009 -    2.018: 0
       2.018 -    3.026: 1
       3.026 -    4.035: 1
       4.035 -    5.044: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CB  ILE A  78 "
            model="   5" pdb=" CA  ILE A  78 "
            model="   5" pdb=" CG1 ILE A  78 "
            model="   5" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.40    5.04 2.00e-01 2.50e+01 6.36e+02
  chirality model="   5" pdb=" CA  HIS A 139 "
            model="   5" pdb=" N   HIS A 139 "
            model="   5" pdb=" C   HIS A 139 "
            model="   5" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.43    4.94 2.00e-01 2.50e+01 6.11e+02
  chirality model="   5" pdb=" CA  SER A  97 "
            model="   5" pdb=" N   SER A  97 "
            model="   5" pdb=" C   SER A  97 "
            model="   5" pdb=" CB  SER A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.39    4.90 2.00e-01 2.50e+01 6.01e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  91 "   -0.138 2.00e-02 2.50e+03   6.20e-02 1.15e+02
        model="   5" pdb=" CG  TYR A  91 "    0.039 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  91 "    0.022 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  91 "    0.054 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  91 "    0.008 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  91 "   -0.024 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  91 "   -0.005 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  91 "   -0.011 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  91 "    0.019 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  91 "    0.115 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  91 "    0.008 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  91 "   -0.088 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  12 "    0.100 2.00e-02 2.50e+03   4.51e-02 6.11e+01
        model="   5" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  12 "   -0.024 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  12 "    0.094 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  12 "   -0.044 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  12 "   -0.023 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  12 "   -0.038 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  89 "    0.074 2.00e-02 2.50e+03   3.82e-02 4.37e+01
        model="   5" pdb=" CG  TYR A  89 "   -0.031 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  89 "   -0.034 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  89 "    0.013 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  89 "   -0.016 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  89 "    0.007 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  89 "    0.027 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  89 "   -0.066 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  89 "    0.022 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  89 "    0.048 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  89 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.03: 39
        2.03 -     2.67: 3098
        2.67 -     3.31: 6578
        3.31 -     3.96: 7907
        3.96 -     4.60: 12064
  Nonbonded interactions: 29686
  Sorted by model distance:
  nonbonded model="   5" pdb=" H   TYR A  89 "
            model="   5" pdb=" HA  TYR A  89 "
     model   vdw
     1.384 1.816
  nonbonded model="   5" pdb=" H   GLY A  80 "
            model="   5" pdb=" HB2 TYR A  81 "
     model   vdw
     1.737 2.270
  nonbonded model="   5" pdb=" HB3 ASP A  74 "
            model="   5" pdb=" H   ILE A  77 "
     model   vdw
     1.794 2.270
  nonbonded model="   5" pdb=" O   LEU A  61 "
            model="   5" pdb=" HG  SER A  65 "
     model   vdw
     1.796 1.850
  nonbonded model="   5" pdb=" HB  ILE A  78 "
            model="   5" pdb=" H   LYS A  79 "
     model   vdw
     1.820 2.270
  ... (remaining 29681 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.16
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  PRO A  52 "
        model="   5" pdb=" CB  ILE A  78 "
        model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CB  TYR A  89 "
        model="   5" pdb=" CB  THR A  92 "
        model="   5" pdb=" CB  LEU A  93 "
        model="   5" pdb=" CB  SER A  97 "
        model="   5" pdb=" CB  LEU A 119 "
        model="   5" pdb=" CB  GLU A 123 "
        model="   5" pdb=" CB  VAL A 126 "
        model="   5" pdb=" CB  ARG A 127 "
        model="   5" pdb=" CB  MET A 128 "
        model="   5" pdb=" CB  SER A 130 "
  Number of C-beta restraints generated:  236

  Time building geometry restraints manager: 1.29 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.69 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (65.435, 42.775, 48.283, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 88
        1.23 -     1.42: 384
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" CD2 HIS A 139 "
       model="  13" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.39e+00
  bond model="  13" pdb=" CD2 HIS A 137 "
       model="  13" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.16e+00
  bond model="  13" pdb=" ND1 HIS A 134 "
       model="  13" pdb=" CE1 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.22e+00
  bond model="  13" pdb=" ND1 HIS A 135 "
       model="  13" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 5.02e+00
  bond model="  13" pdb=" ND1 HIS A 136 "
       model="  13" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.91e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       97.04 -   103.42: 22
      103.42 -   109.80: 2016
      109.80 -   116.17: 962
      116.17 -   122.55: 776
      122.55 -   128.93: 303
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" CA  ASP A 116 "
        model="  13" pdb=" CB  ASP A 116 "
        model="  13" pdb=" CG  ASP A 116 "
      ideal   model   delta    sigma   weight residual
     112.60  117.51   -4.91 1.00e+00 1.00e+00 2.41e+01
  angle model="  13" pdb=" CA  GLU A  84 "
        model="  13" pdb=" CB  GLU A  84 "
        model="  13" pdb=" CG  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     114.10  123.63   -9.53 2.00e+00 2.50e-01 2.27e+01
  angle model="  13" pdb=" OD1 ASN A  72 "
        model="  13" pdb=" CG  ASN A  72 "
        model="  13" pdb=" ND2 ASN A  72 "
      ideal   model   delta    sigma   weight residual
     122.60  117.96    4.64 1.00e+00 1.00e+00 2.15e+01
  angle model="  13" pdb=" CB  HIS A  43 "
        model="  13" pdb=" CG  HIS A  43 "
        model="  13" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  125.81    5.39 1.30e+00 5.92e-01 1.72e+01
  angle model="  13" pdb=" OE1 GLN A 100 "
        model="  13" pdb=" CD  GLN A 100 "
        model="  13" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.46    4.14 1.00e+00 1.00e+00 1.71e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 969
       17.59 -    35.18: 35
       35.18 -    52.78: 16
       52.78 -    70.37: 7
       70.37 -    87.96: 6
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  13" pdb=" C   VAL A  14 "
           model="  13" pdb=" N   VAL A  14 "
           model="  13" pdb=" CA  VAL A  14 "
           model="  13" pdb=" CB  VAL A  14 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.10   13.10     0      2.50e+00 1.60e-01 2.75e+01
  dihedral model="  13" pdb=" N   VAL A  14 "
           model="  13" pdb=" C   VAL A  14 "
           model="  13" pdb=" CA  VAL A  14 "
           model="  13" pdb=" CB  VAL A  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  134.98  -11.58     0      2.50e+00 1.60e-01 2.15e+01
  dihedral model="  13" pdb=" C   THR A  83 "
           model="  13" pdb=" N   THR A  83 "
           model="  13" pdb=" CA  THR A  83 "
           model="  13" pdb=" CB  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.42   11.42     0      2.50e+00 1.60e-01 2.09e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 104
       0.080 -    0.160: 58
       0.160 -    0.239: 7
       0.239 -    0.319: 3
       0.319 -    0.398: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  VAL A  14 "
            model="  13" pdb=" N   VAL A  14 "
            model="  13" pdb=" C   VAL A  14 "
            model="  13" pdb=" CB  VAL A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.04    0.40 2.00e-01 2.50e+01 3.97e+00
  chirality model="  13" pdb=" CA  THR A  83 "
            model="  13" pdb=" N   THR A  83 "
            model="  13" pdb=" C   THR A  83 "
            model="  13" pdb=" CB  THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.14    0.39 2.00e-01 2.50e+01 3.77e+00
  chirality model="  13" pdb=" CA  HIS A 139 "
            model="  13" pdb=" N   HIS A 139 "
            model="  13" pdb=" C   HIS A 139 "
            model="  13" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.19e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  91 "    0.256 2.00e-02 2.50e+03   1.16e-01 4.01e+02
        model="  13" pdb=" CG  TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  91 "   -0.037 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  91 "   -0.070 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  91 "   -0.054 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  91 "   -0.017 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  91 "    0.022 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  91 "    0.219 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  91 "   -0.044 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  91 "   -0.145 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  91 "   -0.116 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  91 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A 111 "   -0.149 2.00e-02 2.50e+03   6.56e-02 1.29e+02
        model="  13" pdb=" CG  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A 111 "    0.024 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A 111 "    0.037 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A 111 "    0.028 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A 111 "   -0.131 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A 111 "    0.031 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A 111 "    0.069 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A 111 "    0.057 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A 111 "    0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  81 "    0.088 2.00e-02 2.50e+03   5.58e-02 9.33e+01
        model="  13" pdb=" CG  TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  81 "   -0.030 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  81 "   -0.031 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  81 "   -0.017 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  81 "    0.144 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  81 "   -0.026 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  81 "   -0.020 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  81 "   -0.048 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  81 "   -0.052 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 340
        2.30 -     2.88: 5108
        2.88 -     3.45: 5363
        3.45 -     4.03: 7135
        4.03 -     4.60: 10636
  Nonbonded interactions: 28582
  Sorted by model distance:
  nonbonded model="  13" pdb=" OD2 ASP A  44 "
            model="  13" pdb=" HG  SER A  46 "
     model   vdw
     1.730 1.850
  nonbonded model="  13" pdb=" OD2 ASP A  74 "
            model="  13" pdb=" HG  SER A  76 "
     model   vdw
     1.737 1.850
  nonbonded model="  13" pdb=" OE1 GLU A  24 "
            model="  13" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.839 1.850
  nonbonded model="  13" pdb=" OD1 ASP A  36 "
            model="  13" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.839 1.850
  nonbonded model="  13" pdb=" O   ASP A  95 "
            model="  13" pdb=" HG  SER A  98 "
     model   vdw
     1.851 1.850
  ... (remaining 28577 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 69
        1.23 -     1.43: 404
        1.43 -     1.62: 657
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" N   LYS A  79 "
       model="   5" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.564 -0.106 1.90e-02 2.77e+03 3.14e+01
  bond model="   5" pdb=" CA  LYS A 125 "
       model="   5" pdb=" CB  LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.530  1.629 -0.099 2.00e-02 2.50e+03 2.45e+01
  bond model="   5" pdb=" N   TYR A  89 "
       model="   5" pdb=" CA  TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.542 -0.084 1.90e-02 2.77e+03 1.96e+01
  bond model="   5" pdb=" C   TYR A  89 "
       model="   5" pdb=" N   SER A  90 "
    ideal  model  delta    sigma   weight residual
    1.329  1.384 -0.055 1.40e-02 5.10e+03 1.52e+01
  bond model="   5" pdb=" C   ALA A 124 "
       model="   5" pdb=" N   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.329  1.382 -0.053 1.40e-02 5.10e+03 1.43e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       68.16 -    83.11: 1
       83.11 -    98.07: 14
       98.07 -   113.02: 2663
      113.02 -   127.98: 1374
      127.98 -   142.93: 27
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" N   LYS A 125 "
        model="   5" pdb=" CA  LYS A 125 "
        model="   5" pdb=" HA  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     110.00   68.16   41.84 3.00e+00 1.11e-01 1.95e+02
  angle model="   5" pdb=" C   ILE A  78 "
        model="   5" pdb=" N   LYS A  79 "
        model="   5" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  142.93  -21.23 1.80e+00 3.09e-01 1.39e+02
  angle model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CG  LYS A  79 "
        model="   5" pdb=" CD  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     111.30  137.52  -26.22 2.30e+00 1.89e-01 1.30e+02
  angle model="   5" pdb=" C   LYS A 125 "
        model="   5" pdb=" CA  LYS A 125 "
        model="   5" pdb=" CB  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     110.10   88.50   21.60 1.90e+00 2.77e-01 1.29e+02
  angle model="   5" pdb=" CG  LYS A  79 "
        model="   5" pdb=" CD  LYS A  79 "
        model="   5" pdb=" CE  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     111.30  137.31  -26.01 2.30e+00 1.89e-01 1.28e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.89: 920
       22.89 -    45.79: 63
       45.79 -    68.68: 16
       68.68 -    91.58: 3
       91.58 -   114.47: 3
  Dihedral angle restraints: 1005
    sinusoidal: 562
      harmonic: 443
  Sorted by residual:
  dihedral model="   5" pdb=" CA  THR A  92 "
           model="   5" pdb=" C   THR A  92 "
           model="   5" pdb=" N   LEU A  93 "
           model="   5" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -65.53 -114.47     0      5.00e+00 4.00e-02 5.24e+02
  dihedral model="   5" pdb=" CA  ILE A  51 "
           model="   5" pdb=" C   ILE A  51 "
           model="   5" pdb=" N   PRO A  52 "
           model="   5" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -65.69 -114.31     0      5.00e+00 4.00e-02 5.23e+02
  dihedral model="   5" pdb=" CA  LYS A 125 "
           model="   5" pdb=" C   LYS A 125 "
           model="   5" pdb=" N   VAL A 126 "
           model="   5" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -72.68 -107.32     0      5.00e+00 4.00e-02 4.61e+02
  ... (remaining 1002 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.122: 160
       1.122 -    2.244: 0
       2.244 -    3.366: 0
       3.366 -    4.487: 4
       4.487 -    5.609: 12
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CA  LYS A  79 "
            model="   5" pdb=" N   LYS A  79 "
            model="   5" pdb=" C   LYS A  79 "
            model="   5" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.10    5.61 2.00e-01 2.50e+01 7.87e+02
  chirality model="   5" pdb=" CA  LEU A  93 "
            model="   5" pdb=" N   LEU A  93 "
            model="   5" pdb=" C   LEU A  93 "
            model="   5" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.85    5.36 2.00e-01 2.50e+01 7.18e+02
  chirality model="   5" pdb=" CB  ILE A  78 "
            model="   5" pdb=" CA  ILE A  78 "
            model="   5" pdb=" CG1 ILE A  78 "
            model="   5" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.57    5.21 2.00e-01 2.50e+01 6.79e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  12 "    0.140 2.00e-02 2.50e+03   6.03e-02 1.09e+02
        model="   5" pdb=" CG  TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  12 "   -0.034 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  12 "   -0.025 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  12 "   -0.023 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  12 "    0.118 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  12 "   -0.061 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  12 "   -0.036 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  12 "   -0.043 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" C   ILE A  51 "    0.089 5.00e-02 4.00e+02   1.32e-01 2.79e+01
        model="   5" pdb=" N   PRO A  52 "   -0.229 5.00e-02 4.00e+02
        model="   5" pdb=" CA  PRO A  52 "    0.070 5.00e-02 4.00e+02
        model="   5" pdb=" CD  PRO A  52 "    0.069 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CA  LEU A  93 "   -0.026 2.00e-02 2.50e+03   5.27e-02 2.78e+01
        model="   5" pdb=" C   LEU A  93 "    0.091 2.00e-02 2.50e+03
        model="   5" pdb=" O   LEU A  93 "   -0.035 2.00e-02 2.50e+03
        model="   5" pdb=" N   GLY A  94 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.41 -     2.05: 81
        2.05 -     2.69: 3317
        2.69 -     3.33: 6795
        3.33 -     3.96: 8013
        3.96 -     4.60: 12205
  Nonbonded interactions: 30411
  Sorted by model distance:
  nonbonded model="   5" pdb=" H   GLU A 123 "
            model="   5" pdb=" HB2 LYS A 125 "
     model   vdw
     1.414 2.270
  nonbonded model="   5" pdb=" HA  TYR A  89 "
            model="   5" pdb=" H   LYS A 101 "
     model   vdw
     1.426 2.270
  nonbonded model="   5" pdb=" HE2 LYS A  79 "
            model="   5" pdb=" HA3 GLY A  80 "
     model   vdw
     1.618 2.440
  nonbonded model="   5" pdb=" H   TYR A  89 "
            model="   5" pdb=" H   LYS A 101 "
     model   vdw
     1.654 2.100
  nonbonded model="   5" pdb="HG23 VAL A  41 "
            model="   5" pdb=" H   HIS A  43 "
     model   vdw
     1.697 2.270
  ... (remaining 30406 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ILE A  77 "
        model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CB  TYR A  89 "
        model="   2" pdb=" CB  TYR A  91 "
        model="   2" pdb=" CB  THR A  92 "
        model="   2" pdb=" CB  SER A  97 "
        model="   2" pdb=" CB  SER A  98 "
        model="   2" pdb=" CB  VAL A 126 "
        model="   2" pdb=" CB  ARG A 127 "
  Number of C-beta restraints generated:  244

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.613, 50.441, 39.449, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.542, 52.16, 39.274, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (85.368, 58.808, 43.403, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 67
        1.23 -     1.43: 408
        1.43 -     1.62: 654
        1.62 -     1.82: 7
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" N   LYS A  79 "
       model="   2" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.623 -0.165 1.90e-02 2.77e+03 7.57e+01
  bond model="   2" pdb=" C   ILE A  78 "
       model="   2" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.425 -0.096 1.40e-02 5.10e+03 4.66e+01
  bond model="   2" pdb=" CA  ILE A  78 "
       model="   2" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.649 -0.124 2.10e-02 2.27e+03 3.46e+01
  bond model="   2" pdb=" N   THR A  92 "
       model="   2" pdb=" CA  THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.458  1.562 -0.104 1.90e-02 2.77e+03 2.97e+01
  bond model="   2" pdb=" C   LYS A  79 "
       model="   2" pdb=" N   GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.329  1.268  0.061 1.40e-02 5.10e+03 1.90e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       60.66 -    76.76: 1
       76.76 -    92.85: 7
       92.85 -   108.95: 1013
      108.95 -   125.05: 2971
      125.05 -   141.15: 87
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" CA  ILE A  78 "
        model="   2" pdb=" CB  ILE A  78 "
        model="   2" pdb=" HB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   60.66   48.34 3.00e+00 1.11e-01 2.60e+02
  angle model="   2" pdb=" CA  ILE A  78 "
        model="   2" pdb=" CB  ILE A  78 "
        model="   2" pdb=" CG2 ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.50  135.81  -25.31 1.70e+00 3.46e-01 2.22e+02
  angle model="   2" pdb=" CG1 ILE A  78 "
        model="   2" pdb=" CB  ILE A  78 "
        model="   2" pdb=" HB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00  141.15  -32.15 3.00e+00 1.11e-01 1.15e+02
  angle model="   2" pdb=" C   LYS A  79 "
        model="   2" pdb=" N   GLY A  80 "
        model="   2" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  106.28   15.42 1.80e+00 3.09e-01 7.34e+01
  angle model="   2" pdb=" CA  VAL A 126 "
        model="   2" pdb=" C   VAL A 126 "
        model="   2" pdb=" N   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     116.20   99.39   16.81 2.00e+00 2.50e-01 7.06e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.78: 936
       21.78 -    43.56: 54
       43.56 -    65.34: 16
       65.34 -    87.12: 3
       87.12 -   108.89: 4
  Dihedral angle restraints: 1013
    sinusoidal: 562
      harmonic: 451
  Sorted by residual:
  dihedral model="   2" pdb=" CA  LYS A  79 "
           model="   2" pdb=" C   LYS A  79 "
           model="   2" pdb=" N   GLY A  80 "
           model="   2" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   71.11  108.89     0      5.00e+00 4.00e-02 4.74e+02
  dihedral model="   2" pdb=" CA  THR A  92 "
           model="   2" pdb=" C   THR A  92 "
           model="   2" pdb=" N   LEU A  93 "
           model="   2" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   74.34  105.66     0      5.00e+00 4.00e-02 4.47e+02
  dihedral model="   2" pdb=" CA  SER A  76 "
           model="   2" pdb=" C   SER A  76 "
           model="   2" pdb=" N   ILE A  77 "
           model="   2" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   84.70   95.30     0      5.00e+00 4.00e-02 3.63e+02
  ... (remaining 1010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.007: 164
       1.007 -    2.012: 0
       2.012 -    3.018: 0
       3.018 -    4.023: 3
       4.023 -    5.029: 9
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CB  THR A  92 "
            model="   2" pdb=" CA  THR A  92 "
            model="   2" pdb=" OG1 THR A  92 "
            model="   2" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.48    5.03 2.00e-01 2.50e+01 6.32e+02
  chirality model="   2" pdb=" CA  TYR A  89 "
            model="   2" pdb=" N   TYR A  89 "
            model="   2" pdb=" C   TYR A  89 "
            model="   2" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.37    4.88 2.00e-01 2.50e+01 5.94e+02
  chirality model="   2" pdb=" CA  TYR A  91 "
            model="   2" pdb=" N   TYR A  91 "
            model="   2" pdb=" C   TYR A  91 "
            model="   2" pdb=" CB  TYR A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.34    4.85 2.00e-01 2.50e+01 5.87e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  89 "    0.175 2.00e-02 2.50e+03   7.05e-02 1.49e+02
        model="   2" pdb=" CG  TYR A  89 "   -0.022 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  89 "   -0.040 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  89 "   -0.038 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  89 "   -0.016 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  89 "   -0.019 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  89 "    0.018 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  89 "    0.122 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  89 "   -0.068 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  89 "   -0.061 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  89 "   -0.022 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  89 "   -0.031 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  PHE A  67 "    0.142 2.00e-02 2.50e+03   5.55e-02 9.26e+01
        model="   2" pdb=" CG  PHE A  67 "   -0.029 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 PHE A  67 "   -0.036 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 PHE A  67 "   -0.034 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 PHE A  67 "   -0.005 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 PHE A  67 "   -0.006 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  PHE A  67 "    0.029 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 PHE A  67 "   -0.060 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 PHE A  67 "   -0.057 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 PHE A  67 "   -0.008 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 PHE A  67 "   -0.012 2.00e-02 2.50e+03
        model="   2" pdb=" HZ  PHE A  67 "    0.076 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  91 "    0.100 2.00e-02 2.50e+03   3.82e-02 4.38e+01
        model="   2" pdb=" CG  TYR A  91 "   -0.025 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  91 "   -0.022 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  91 "   -0.025 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  91 "   -0.005 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  91 "    0.055 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  91 "   -0.029 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  91 "   -0.040 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.13: 114
        2.13 -     2.75: 3862
        2.75 -     3.37: 6524
        3.37 -     3.98: 7949
        3.98 -     4.60: 11796
  Nonbonded interactions: 30245
  Sorted by model distance:
  nonbonded model="   2" pdb=" HA  ARG A 127 "
            model="   2" pdb=" H   ARG A 129 "
     model   vdw
     1.515 2.270
  nonbonded model="   2" pdb="HG23 THR A  92 "
            model="   2" pdb=" H   LEU A  99 "
     model   vdw
     1.524 2.270
  nonbonded model="   2" pdb=" HA  ILE A  78 "
            model="   2" pdb=" HB  ILE A  78 "
     model   vdw
     1.594 1.952
  nonbonded model="   2" pdb="HG22 ILE A  78 "
            model="   2" pdb=" HA2 GLY A  80 "
     model   vdw
     1.631 2.440
  nonbonded model="   2" pdb=" HA  VAL A 126 "
            model="   2" pdb=" H   ARG A 127 "
     model   vdw
     1.652 2.270
  ... (remaining 30240 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 128}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  ILE A  77 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CB  TYR A  89 "
        model="   1" pdb=" CB  THR A  92 "
        model="   1" pdb=" CB  LEU A  93 "
        model="   1" pdb=" CB  SER A  98 "
        model="   1" pdb=" CB  LYS A 125 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.23 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 130}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1105
        1.03 -     1.23: 56
        1.23 -     1.43: 417
        1.43 -     1.62: 658
        1.62 -     1.82: 5
  Bond restraints: 2241
  Sorted by residual:
  bond model="   1" pdb=" CA  LYS A  79 "
       model="   1" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.624 -0.099 2.10e-02 2.27e+03 2.23e+01
  bond model="   1" pdb=" N   GLY A  80 "
       model="   1" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.505 -0.054 1.60e-02 3.91e+03 1.15e+01
  bond model="   1" pdb=" C   TYR A  89 "
       model="   1" pdb=" N   SER A  90 "
    ideal  model  delta    sigma   weight residual
    1.329  1.289  0.040 1.40e-02 5.10e+03 8.01e+00
  bond model="   1" pdb=" CA  THR A  92 "
       model="   1" pdb=" C   THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.525  1.583 -0.058 2.10e-02 2.27e+03 7.69e+00
  bond model="   1" pdb=" CZ  ARG A  21 "
       model="   1" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.35e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       89.00 -    99.78: 11
       99.78 -   110.57: 2232
      110.57 -   121.35: 1363
      121.35 -   132.13: 467
      132.13 -   142.91: 4
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   1" pdb=" C   TYR A  89 "
        model="   1" pdb=" N   SER A  90 "
        model="   1" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  142.91  -21.21 1.80e+00 3.09e-01 1.39e+02
  angle model="   1" pdb=" C   SER A  98 "
        model="   1" pdb=" N   LEU A  99 "
        model="   1" pdb=" CA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     121.70  137.59  -15.89 1.80e+00 3.09e-01 7.80e+01
  angle model="   1" pdb=" CA  VAL A 126 "
        model="   1" pdb=" C   VAL A 126 "
        model="   1" pdb=" N   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     116.20  100.59   15.61 2.00e+00 2.50e-01 6.09e+01
  angle model="   1" pdb=" CD1 LEU A  93 "
        model="   1" pdb=" CG  LEU A  93 "
        model="   1" pdb=" CD2 LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.80  127.91  -17.11 2.20e+00 2.07e-01 6.05e+01
  angle model="   1" pdb=" O   TYR A  89 "
        model="   1" pdb=" C   TYR A  89 "
        model="   1" pdb=" N   SER A  90 "
      ideal   model   delta    sigma   weight residual
     123.00  111.12   11.88 1.60e+00 3.91e-01 5.52e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.60: 965
       26.60 -    53.19: 41
       53.19 -    79.79: 8
       79.79 -   106.38: 1
      106.38 -   132.98: 1
  Dihedral angle restraints: 1016
    sinusoidal: 561
      harmonic: 455
  Sorted by residual:
  dihedral model="   1" pdb=" CA  ALA A 124 "
           model="   1" pdb=" C   ALA A 124 "
           model="   1" pdb=" N   LYS A 125 "
           model="   1" pdb=" CA  LYS A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   47.02  132.98     0      5.00e+00 4.00e-02 7.07e+02
  dihedral model="   1" pdb=" CA  THR A  92 "
           model="   1" pdb=" C   THR A  92 "
           model="   1" pdb=" N   LEU A  93 "
           model="   1" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -101.37  -78.63     0      5.00e+00 4.00e-02 2.47e+02
  dihedral model="   1" pdb=" CA  ILE A  78 "
           model="   1" pdb=" C   ILE A  78 "
           model="   1" pdb=" N   LYS A  79 "
           model="   1" pdb=" CA  LYS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  116.33   63.67     0      5.00e+00 4.00e-02 1.62e+02
  ... (remaining 1013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.122: 166
       1.122 -    2.243: 0
       2.243 -    3.364: 0
       3.364 -    4.484: 2
       4.484 -    5.605: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  LEU A  93 "
            model="   1" pdb=" N   LEU A  93 "
            model="   1" pdb=" C   LEU A  93 "
            model="   1" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.09    5.61 2.00e-01 2.50e+01 7.86e+02
  chirality model="   1" pdb=" CB  ILE A  77 "
            model="   1" pdb=" CA  ILE A  77 "
            model="   1" pdb=" CG1 ILE A  77 "
            model="   1" pdb=" CG2 ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.59    5.24 2.00e-01 2.50e+01 6.86e+02
  chirality model="   1" pdb=" CA  THR A  92 "
            model="   1" pdb=" N   THR A  92 "
            model="   1" pdb=" C   THR A  92 "
            model="   1" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.71    5.23 2.00e-01 2.50e+01 6.85e+02
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  12 "    0.138 2.00e-02 2.50e+03   5.91e-02 1.05e+02
        model="   1" pdb=" CG  TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  12 "   -0.030 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  12 "    0.117 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  12 "   -0.050 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  12 "   -0.045 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  12 "   -0.029 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  12 "   -0.033 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  50 "   -0.121 2.00e-02 2.50e+03   4.99e-02 7.46e+01
        model="   1" pdb=" CG  TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  50 "    0.032 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  50 "   -0.087 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  50 "    0.057 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  50 "    0.037 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  PHE A  15 "    0.120 2.00e-02 2.50e+03   4.67e-02 6.55e+01
        model="   1" pdb=" CG  PHE A  15 "   -0.027 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 PHE A  15 "   -0.030 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 PHE A  15 "   -0.031 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 PHE A  15 "   -0.005 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 PHE A  15 "   -0.004 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  PHE A  15 "    0.024 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 PHE A  15 "   -0.047 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 PHE A  15 "   -0.050 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 PHE A  15 "   -0.008 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 PHE A  15 "   -0.004 2.00e-02 2.50e+03
        model="   1" pdb=" HZ  PHE A  15 "    0.062 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 201
        2.21 -     2.81: 4510
        2.81 -     3.41: 6437
        3.41 -     4.00: 7991
        4.00 -     4.60: 11985
  Nonbonded interactions: 31124
  Sorted by model distance:
  nonbonded model="   1" pdb="HG12 VAL A  41 "
            model="   1" pdb="HG12 VAL A 112 "
     model   vdw
     1.614 2.440
  nonbonded model="   1" pdb=" HA  LYS A 125 "
            model="   1" pdb=" H   ARG A 127 "
     model   vdw
     1.658 2.270
  nonbonded model="   1" pdb=" H   THR A  92 "
            model="   1" pdb=" H   GLN A 100 "
     model   vdw
     1.661 2.100
  nonbonded model="   1" pdb=" HA  THR A  92 "
            model="   1" pdb=" HA  SER A  98 "
     model   vdw
     1.664 2.440
  nonbonded model="   1" pdb=" HA  ILE A 122 "
            model="   1" pdb=" H   LYS A 125 "
     model   vdw
     1.679 2.270
  ... (remaining 31119 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  ILE A  77 "
        model="   1" pdb=" CB  TYR A  89 "
        model="   1" pdb=" CB  SER A  97 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CB  TYR A  89 "
        model="   6" pdb=" CB  THR A  92 "
        model="   6" pdb=" CB  SER A  97 "
        model="   6" pdb=" CB  SER A  98 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 0.86 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CB  ASP A  74 "
        model="   3" pdb=" CB  ILE A  78 "
        model="   3" pdb=" CB  LYS A  79 "
        model="   3" pdb=" CB  TYR A  89 "
        model="   3" pdb=" CB  THR A  92 "
        model="   3" pdb=" CB  LEU A  93 "
        model="   3" pdb=" CB  LEU A 119 "
        model="   3" pdb=" CB  ILE A 122 "
        model="   3" pdb=" CB  GLU A 123 "
  Number of C-beta restraints generated:  244

  Time building geometry restraints manager: 1.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CB  LEU A  93 "
  Number of C-beta restraints generated:  258

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 0.68, per 1000 atoms: 0.31
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.466, 80.337, 46.663, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 53
        1.23 -     1.43: 420
        1.43 -     1.62: 658
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   1" pdb=" N   GLY A  80 "
       model="   1" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.606 -0.155 1.60e-02 3.91e+03 9.34e+01
  bond model="   1" pdb=" CA  LYS A  79 "
       model="   1" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.659 -0.134 2.10e-02 2.27e+03 4.07e+01
  bond model="   1" pdb=" C   TYR A  89 "
       model="   1" pdb=" N   SER A  90 "
    ideal  model  delta    sigma   weight residual
    1.329  1.398 -0.069 1.40e-02 5.10e+03 2.43e+01
  bond model="   1" pdb=" C   ILE A  78 "
       model="   1" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.271  0.058 1.40e-02 5.10e+03 1.71e+01
  bond model="   1" pdb=" N   TYR A  89 "
       model="   1" pdb=" CA  TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.534 -0.076 1.90e-02 2.77e+03 1.62e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       78.71 -    91.05: 3
       91.05 -   103.39: 53
      103.39 -   115.73: 2925
      115.73 -   128.08: 1081
      128.08 -   140.42: 17
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   1" pdb=" C   LEU A  93 "
        model="   1" pdb=" N   GLY A  94 "
        model="   1" pdb=" CA  GLY A  94 "
      ideal   model   delta    sigma   weight residual
     121.70  140.42  -18.72 1.80e+00 3.09e-01 1.08e+02
  angle model="   1" pdb=" C   LEU A  99 "
        model="   1" pdb=" CA  LEU A  99 "
        model="   1" pdb=" HA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     109.00   78.71   30.29 3.00e+00 1.11e-01 1.02e+02
  angle model="   1" pdb=" CA  LYS A  79 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CG  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     114.10  133.78  -19.68 2.00e+00 2.50e-01 9.69e+01
  angle model="   1" pdb=" CA  LYS A  79 "
        model="   1" pdb=" C   LYS A  79 "
        model="   1" pdb=" N   GLY A  80 "
      ideal   model   delta    sigma   weight residual
     116.20  135.82  -19.62 2.00e+00 2.50e-01 9.62e+01
  angle model="   1" pdb=" N   ILE A  78 "
        model="   1" pdb=" CA  ILE A  78 "
        model="   1" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.00   82.59   27.41 3.00e+00 1.11e-01 8.35e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.60: 972
       25.60 -    51.20: 48
       51.20 -    76.80: 4
       76.80 -   102.40: 0
      102.40 -   127.99: 1
  Dihedral angle restraints: 1025
    sinusoidal: 562
      harmonic: 463
  Sorted by residual:
  dihedral model="   1" pdb=" CA  ILE A  78 "
           model="   1" pdb=" C   ILE A  78 "
           model="   1" pdb=" N   LYS A  79 "
           model="   1" pdb=" CA  LYS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -52.01 -127.99     0      5.00e+00 4.00e-02 6.55e+02
  dihedral model="   1" pdb=" C   LEU A  99 "
           model="   1" pdb=" N   LEU A  99 "
           model="   1" pdb=" CA  LEU A  99 "
           model="   1" pdb=" CB  LEU A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -165.45   42.85     0      2.50e+00 1.60e-01 2.94e+02
  dihedral model="   1" pdb=" N   LEU A  99 "
           model="   1" pdb=" C   LEU A  99 "
           model="   1" pdb=" CA  LEU A  99 "
           model="   1" pdb=" CB  LEU A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  163.31  -40.51     0      2.50e+00 1.60e-01 2.63e+02
  ... (remaining 1022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.997: 168
       0.997 -    1.993: 3
       1.993 -    2.989: 0
       2.989 -    3.985: 1
       3.985 -    4.981: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  ILE A  77 "
            model="   1" pdb=" N   ILE A  77 "
            model="   1" pdb=" C   ILE A  77 "
            model="   1" pdb=" CB  ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -2.55    4.98 2.00e-01 2.50e+01 6.20e+02
  chirality model="   1" pdb=" CB  ILE A  77 "
            model="   1" pdb=" CA  ILE A  77 "
            model="   1" pdb=" CG1 ILE A  77 "
            model="   1" pdb=" CG2 ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.30    4.94 2.00e-01 2.50e+01 6.10e+02
  chirality model="   1" pdb=" CA  TYR A  89 "
            model="   1" pdb=" N   TYR A  89 "
            model="   1" pdb=" C   TYR A  89 "
            model="   1" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.04    4.55 2.00e-01 2.50e+01 5.18e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CA  ILE A  78 "    0.044 2.00e-02 2.50e+03   8.49e-02 7.20e+01
        model="   1" pdb=" C   ILE A  78 "   -0.147 2.00e-02 2.50e+03
        model="   1" pdb=" O   ILE A  78 "    0.055 2.00e-02 2.50e+03
        model="   1" pdb=" N   LYS A  79 "    0.048 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  50 "   -0.120 2.00e-02 2.50e+03   4.57e-02 6.28e+01
        model="   1" pdb=" CG  TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  50 "    0.030 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  50 "   -0.063 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  50 "    0.042 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  50 "    0.048 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  12 "    0.082 2.00e-02 2.50e+03   3.96e-02 4.71e+01
        model="   1" pdb=" CG  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  12 "    0.087 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  12 "   -0.037 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  12 "   -0.040 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 81
        2.09 -     2.72: 3538
        2.72 -     3.34: 6567
        3.34 -     3.97: 7935
        3.97 -     4.60: 12007
  Nonbonded interactions: 30128
  Sorted by model distance:
  nonbonded model="   1" pdb=" HA  LYS A  79 "
            model="   1" pdb=" HA  LEU A  93 "
     model   vdw
     1.461 2.440
  nonbonded model="   1" pdb=" OD1 ASP A  44 "
            model="   1" pdb=" HG  SER A  46 "
     model   vdw
     1.740 1.850
  nonbonded model="   1" pdb=" OD2 ASP A  74 "
            model="   1" pdb=" HH  TYR A  91 "
     model   vdw
     1.774 1.850
  nonbonded model="   1" pdb=" H   ILE A  78 "
            model="   1" pdb="HG13 ILE A  78 "
     model   vdw
     1.821 2.270
  nonbonded model="   1" pdb=" O   LEU A  61 "
            model="   1" pdb=" HG  SER A  65 "
     model   vdw
     1.828 1.850
  ... (remaining 30123 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.982, 48.192, 42.827, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.05, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.452, 55.902, 45.783, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 49
        1.23 -     1.43: 429
        1.43 -     1.62: 652
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   6" pdb=" N   GLY A  80 "
       model="   6" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.651 -0.200 1.60e-02 3.91e+03 1.56e+02
  bond model="   6" pdb=" CA  LYS A  79 "
       model="   6" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.690 -0.165 2.10e-02 2.27e+03 6.21e+01
  bond model="   6" pdb=" N   SER A  90 "
       model="   6" pdb=" CA  SER A  90 "
    ideal  model  delta    sigma   weight residual
    1.458  1.584 -0.126 1.90e-02 2.77e+03 4.38e+01
  bond model="   6" pdb=" C   LEU A  93 "
       model="   6" pdb=" N   GLY A  94 "
    ideal  model  delta    sigma   weight residual
    1.329  1.273  0.056 1.40e-02 5.10e+03 1.63e+01
  bond model="   6" pdb=" C   LYS A  79 "
       model="   6" pdb=" N   GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.329  1.384 -0.055 1.40e-02 5.10e+03 1.52e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       65.41 -    80.91: 1
       80.91 -    96.41: 5
       96.41 -   111.91: 2530
      111.91 -   127.41: 1517
      127.41 -   142.92: 26
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   6" pdb=" N   TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.00   65.41   44.59 3.00e+00 1.11e-01 2.21e+02
  angle model="   6" pdb=" C   LYS A  79 "
        model="   6" pdb=" N   GLY A  80 "
        model="   6" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  142.92  -21.22 1.80e+00 3.09e-01 1.39e+02
  angle model="   6" pdb=" CB  TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00  140.55  -31.55 3.00e+00 1.11e-01 1.11e+02
  angle model="   6" pdb=" N   TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" C   TYR A  89 "
      ideal   model   delta    sigma   weight residual
     111.00  137.18  -26.18 2.80e+00 1.28e-01 8.74e+01
  angle model="   6" pdb=" N   SER A  90 "
        model="   6" pdb=" CA  SER A  90 "
        model="   6" pdb=" CB  SER A  90 "
      ideal   model   delta    sigma   weight residual
     110.50  124.73  -14.23 1.70e+00 3.46e-01 7.01e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.86: 945
       22.86 -    45.72: 57
       45.72 -    68.57: 16
       68.57 -    91.43: 3
       91.43 -   114.29: 2
  Dihedral angle restraints: 1023
    sinusoidal: 562
      harmonic: 461
  Sorted by residual:
  dihedral model="   6" pdb=" CA  ILE A  78 "
           model="   6" pdb=" C   ILE A  78 "
           model="   6" pdb=" N   LYS A  79 "
           model="   6" pdb=" CA  LYS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -65.71 -114.29     0      5.00e+00 4.00e-02 5.22e+02
  dihedral model="   6" pdb=" CA  SER A  90 "
           model="   6" pdb=" C   SER A  90 "
           model="   6" pdb=" N   TYR A  91 "
           model="   6" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -68.49 -111.51     0      5.00e+00 4.00e-02 4.97e+02
  dihedral model="   6" pdb=" CA  LEU A  99 "
           model="   6" pdb=" C   LEU A  99 "
           model="   6" pdb=" N   GLN A 100 "
           model="   6" pdb=" CA  GLN A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -96.03  -83.97     0      5.00e+00 4.00e-02 2.82e+02
  ... (remaining 1020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.046: 169
       1.046 -    2.091: 0
       2.091 -    3.136: 0
       3.136 -    4.182: 2
       4.182 -    5.227: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CA  THR A  92 "
            model="   6" pdb=" N   THR A  92 "
            model="   6" pdb=" C   THR A  92 "
            model="   6" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.70    5.23 2.00e-01 2.50e+01 6.83e+02
  chirality model="   6" pdb=" CA  SER A  98 "
            model="   6" pdb=" N   SER A  98 "
            model="   6" pdb=" C   SER A  98 "
            model="   6" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.61    5.12 2.00e-01 2.50e+01 6.57e+02
  chirality model="   6" pdb=" CB  ILE A  78 "
            model="   6" pdb=" CA  ILE A  78 "
            model="   6" pdb=" CG1 ILE A  78 "
            model="   6" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.40    5.05 2.00e-01 2.50e+01 6.36e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  PHE A  67 "    0.322 2.00e-02 2.50e+03   1.24e-01 4.64e+02
        model="   6" pdb=" CG  PHE A  67 "   -0.071 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 PHE A  67 "   -0.070 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 PHE A  67 "   -0.091 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 PHE A  67 "   -0.019 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 PHE A  67 "    0.004 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  PHE A  67 "    0.056 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 PHE A  67 "   -0.103 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 PHE A  67 "   -0.166 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 PHE A  67 "   -0.034 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 PHE A  67 "    0.032 2.00e-02 2.50e+03
        model="   6" pdb=" HZ  PHE A  67 "    0.141 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  12 "    0.152 2.00e-02 2.50e+03   6.54e-02 1.28e+02
        model="   6" pdb=" CG  TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  12 "   -0.032 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  12 "   -0.032 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  12 "    0.130 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  12 "   -0.053 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  12 "   -0.054 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  12 "   -0.036 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  12 "   -0.034 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CA  SER A  98 "   -0.043 2.00e-02 2.50e+03   8.96e-02 8.02e+01
        model="   6" pdb=" C   SER A  98 "    0.155 2.00e-02 2.50e+03
        model="   6" pdb=" O   SER A  98 "   -0.062 2.00e-02 2.50e+03
        model="   6" pdb=" N   LEU A  99 "   -0.050 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.41 -     2.05: 55
        2.05 -     2.69: 3323
        2.69 -     3.32: 6815
        3.32 -     3.96: 8381
        3.96 -     4.60: 12563
  Nonbonded interactions: 31137
  Sorted by model distance:
  nonbonded model="   6" pdb="HD12 ILE A  78 "
            model="   6" pdb=" H   LYS A  79 "
     model   vdw
     1.411 2.270
  nonbonded model="   6" pdb=" HA  ILE A  78 "
            model="   6" pdb=" H   GLY A  80 "
     model   vdw
     1.419 2.270
  nonbonded model="   6" pdb=" H   TYR A  89 "
            model="   6" pdb=" HA  TYR A  89 "
     model   vdw
     1.427 1.816
  nonbonded model="   6" pdb="HG22 ILE A  78 "
            model="   6" pdb=" HA  LYS A  79 "
     model   vdw
     1.490 2.440
  nonbonded model="   6" pdb=" H   LEU A  93 "
            model="   6" pdb=" HA  SER A  98 "
     model   vdw
     1.669 2.270
  ... (remaining 31132 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 65
        1.23 -     1.43: 410
        1.43 -     1.62: 656
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   3" pdb=" N   LYS A  79 "
       model="   3" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.570 -0.112 1.90e-02 2.77e+03 3.46e+01
  bond model="   3" pdb=" CA  ALA A 124 "
       model="   3" pdb=" C   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.525  1.634 -0.109 2.10e-02 2.27e+03 2.72e+01
  bond model="   3" pdb=" N   GLY A  80 "
       model="   3" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.515 -0.064 1.60e-02 3.91e+03 1.59e+01
  bond model="   3" pdb=" C   LYS A  79 "
       model="   3" pdb=" N   GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.329  1.383 -0.054 1.40e-02 5.10e+03 1.47e+01
  bond model="   3" pdb=" N   GLY A  94 "
       model="   3" pdb=" CA  GLY A  94 "
    ideal  model  delta    sigma   weight residual
    1.451  1.394  0.057 1.60e-02 3.91e+03 1.28e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       79.78 -    91.07: 5
       91.07 -   102.36: 42
      102.36 -   113.65: 2726
      113.65 -   124.94: 1211
      124.94 -   136.23: 95
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   3" pdb=" N   TYR A  81 "
        model="   3" pdb=" CA  TYR A  81 "
        model="   3" pdb=" CB  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     110.50  131.80  -21.30 1.70e+00 3.46e-01 1.57e+02
  angle model="   3" pdb=" CB  TYR A  89 "
        model="   3" pdb=" CA  TYR A  89 "
        model="   3" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   79.78   29.22 3.00e+00 1.11e-01 9.48e+01
  angle model="   3" pdb=" CA  PHE A  15 "
        model="   3" pdb=" CB  PHE A  15 "
        model="   3" pdb=" CG  PHE A  15 "
      ideal   model   delta    sigma   weight residual
     113.80  104.46    9.34 1.00e+00 1.00e+00 8.73e+01
  angle model="   3" pdb=" C   ALA A 124 "
        model="   3" pdb=" CA  ALA A 124 "
        model="   3" pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     110.50  123.05  -12.55 1.50e+00 4.44e-01 7.01e+01
  angle model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CA  ILE A  51 "
        model="   3" pdb=" HA  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   84.71   24.29 3.00e+00 1.11e-01 6.55e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.74: 934
       24.74 -    49.48: 62
       49.48 -    74.21: 14
       74.21 -    98.95: 2
       98.95 -   123.69: 1
  Dihedral angle restraints: 1013
    sinusoidal: 562
      harmonic: 451
  Sorted by residual:
  dihedral model="   3" pdb=" CA  GLY A  80 "
           model="   3" pdb=" C   GLY A  80 "
           model="   3" pdb=" N   TYR A  81 "
           model="   3" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   56.31  123.69     0      5.00e+00 4.00e-02 6.12e+02
  dihedral model="   3" pdb=" CA  LYS A 125 "
           model="   3" pdb=" C   LYS A 125 "
           model="   3" pdb=" N   VAL A 126 "
           model="   3" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   89.59   90.41     0      5.00e+00 4.00e-02 3.27e+02
  dihedral model="   3" pdb=" CA  THR A  92 "
           model="   3" pdb=" C   THR A  92 "
           model="   3" pdb=" N   LEU A  93 "
           model="   3" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  109.97   70.03     0      5.00e+00 4.00e-02 1.96e+02
  ... (remaining 1010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.101: 162
       1.101 -    2.201: 0
       2.201 -    3.301: 2
       3.301 -    4.401: 1
       4.  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 56
        1.23 -     1.43: 417
        1.43 -     1.62: 659
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" CZ  ARG A  21 "
       model="   5" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.81e+00
  bond model="   5" pdb=" CD2 HIS A 138 "
       model="   5" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.41e+00
  bond model="   5" pdb=" CZ  ARG A  58 "
       model="   5" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.41e+00
  bond model="   5" pdb=" CD2 HIS A 134 "
       model="   5" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.37e+00
  bond model="   5" pdb=" CD2 HIS A 139 "
       model="   5" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.32e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       92.24 -   100.89: 13
      100.89 -   109.54: 1925
      109.54 -   118.19: 1176
      118.19 -   126.84: 936
      126.84 -   135.49: 29
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" N   ASP A  74 "
        model="   5" pdb=" CA  ASP A  74 "
        model="   5" pdb=" CB  ASP A  74 "
      ideal   model   delta    sigma   weight residual
     110.50   96.81   13.69 1.70e+00 3.46e-01 6.48e+01
  angle model="   5" pdb=" C   HIS A 138 "
        model="   5" pdb=" N   HIS A 139 "
        model="   5" pdb=" CA  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     121.70  135.49  -13.79 1.80e+00 3.09e-01 5.87e+01
  angle model="   5" pdb=" C   ASP A  74 "
        model="   5" pdb=" CA  ASP A  74 "
        model="   5" pdb=" CB  ASP A  74 "
      ideal   model   delta    sigma   weight residual
     110.10  124.62  -14.52 1.90e+00 2.77e-01 5.84e+01
  angle model="   5" pdb=" CA  ILE A  51 "
        model="   5" pdb=" C   ILE A  51 "
        model="   5" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  128.00  -11.10 1.50e+00 4.44e-01 5.48e+01
  angle model="   5" pdb=" C   ILE A  78 "
        model="   5" pdb=" N   LYS A  79 "
        model="   5" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  134.59  -12.89 1.80e+00 3.09e-01 5.13e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.64: 912
       14.64 -    29.27: 73
       29.27 -    43.91: 25
       43.91 -    58.55: 13
       58.55 -    73.18: 4
  Dihedral angle restraints: 1027
    sinusoidal: 562
      harmonic: 465
  Sorted by residual:
  dihedral model="   5" pdb=" CA  THR A  92 "
           model="   5" pdb=" C   THR A  92 "
           model="   5" pdb=" N   LEU A  93 "
           model="   5" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  110.31   69.69     0      5.00e+00 4.00e-02 1.94e+02
  dihedral model="   5" pdb=" CA  LEU A 119 "
           model="   5" pdb=" C   LEU A 119 "
           model="   5" pdb=" N   GLU A 120 "
           model="   5" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  121.75   58.25     0      5.00e+00 4.00e-02 1.36e+02
  dihedral model="   5" pdb=" CA  PRO A 117 "
           model="   5" pdb=" C   PRO A 117 "
           model="   5" pdb=" N   ASP A 118 "
           model="   5" pdb=" CA  ASP A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  124.44   55.56     0      5.00e+00 4.00e-02 1.23e+02
  ... (remaining 1024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.003: 173
       1.003 -    2.004: 0
       2.004 -    3.006: 0
       3.006 -    4.008: 1
      401 -    5.501: 11
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   3" pdb=" CA  THR A  92 "
            model="   3" pdb=" N   THR A  92 "
            model="   3" pdb=" C   THR A  92 "
            model="   3" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.98    5.50 2.00e-01 2.50e+01 7.57e+02
  chirality model="   3" pdb=" CA  LYS A  79 "
            model="   3" pdb=" N   LYS A  79 "
            model="   3" pdb=" C   LYS A  79 "
            model="   3" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.87    5.38 2.00e-01 2.50e+01 7.23e+02
  chirality model="   3" pdb=" CA  LEU A  93 "
            model="   3" pdb=" N   LEU A  93 "
            model="   3" pdb=" C   LEU A  93 "
            model="   3" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.75    5.26 2.00e-01 2.50e+01 6.91e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  PHE A  15 "    0.614 2.00e-02 2.50e+03   2.30e-01 1.58e+03
        model="   3" pdb=" CG  PHE A  15 "   -0.123 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 PHE A  15 "   -0.160 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 PHE A  15 "   -0.144 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 PHE A  15 "   -0.011 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  PHE A  15 "    0.083 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 PHE A  15 "   -0.291 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 PHE A  15 "   -0.244 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 PHE A  15 "    0.059 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 PHE A  15 "    0.014 2.00e-02 2.50e+03
        model="   3" pdb=" HZ  PHE A  15 "    0.199 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  81 "   -0.200 2.00e-02 2.50e+03   1.10e-01 3.64e+02
        model="   3" pdb=" CG  TYR A  81 "   -0.033 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  81 "    0.028 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  81 "    0.039 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  81 "    0.053 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  81 "    0.047 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  81 "   -0.008 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  81 "   -0.260 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  81 "    0.053 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  81 "    0.082 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  81 "    0.110 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  81 "    0.088 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  50 "    0.132 2.00e-02 2.50e+03   5.23e-02 8.21e+01
        model="   3" pdb=" CG  TYR A  50 "   -0.025 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  50 "   -0.032 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  50 "    0.089 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  50 "   -0.053 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  50 "   -0.037 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.05: 74
        2.05 -     2.69: 3411
  4.008 -    5.010: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CA  LEU A  93 "
            model="   5" pdb=" N   LEU A  93 "
            model="   5" pdb=" C   LEU A  93 "
            model="   5" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.50    5.01 2.00e-01 2.50e+01 6.27e+02
  chirality model="   5" pdb=" CA  LYS A  79 "
            model="   5" pdb=" N   LYS A  79 "
            model="   5" pdb=" C   LYS A  79 "
            model="   5" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.30    4.81 2.00e-01 2.50e+01 5.80e+02
  chirality model="   5" pdb=" CA  ILE A  51 "
            model="   5" pdb=" N   ILE A  51 "
            model="   5" pdb=" C   ILE A  51 "
            model="   5" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -1.06    3.49 2.00e-01 2.50e+01 3.05e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A 111 "   -0.119 2.00e-02 2.50e+03   4.78e-02 6.85e+01
        model="   5" pdb=" CG  TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A 111 "    0.028 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A 111 "    0.025 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A 111 "   -0.082 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A 111 "    0.045 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A 111 "    0.038 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A 111 "    0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  12 "    0.092 2.00e-02 2.50e+03   4.22e-02 5.35e+01
        model="   5" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  12 "   -0.023 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  12 "    0.088 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  12 "   -0.042 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  12 "   -0.039 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  50 "    0.083 2.00e-02 2.50e+03   3.62e-02 3.93e+01
        model="   5" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  50 "    0.071 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  50 "   -0.036 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  50 "   -0.031 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.10: 76
        2.10 -     2.73: 3592       2.69 -     3.33: 6876
        3.33 -     3.96: 8572
        3.96 -     4.60: 12773
  Nonbonded interactions: 31706
  Sorted by model distance:
  nonbonded model="   3" pdb="HG23 ILE A  78 "
            model="   3" pdb=" H   LEU A  93 "
     model   vdw
     1.418 2.270
  nonbonded model="   3" pdb=" HA  MET A 128 "
            model="   3" pdb=" H   SER A 130 "
     model   vdw
     1.529 2.270
  nonbonded model="   3" pdb=" HA  ALA A 124 "
            model="   3" pdb=" H   VAL A 126 "
     model   vdw
     1.605 2.270
  nonbonded model="   3" pdb=" HB  ILE A  86 "
            model="   3" pdb=" HA  TYR A  89 "
     model   vdw
     1.673 2.440
  nonbonded model="   3" pdb=" HA  ILE A  78 "
            model="   3" pdb=" HA3 GLY A  80 "
     model   vdw
     1.685 2.440
  ... (remaining 31701 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        2.73 -     3.35: 6331
        3.35 -     3.98: 7591
        3.98 -     4.60: 11441
  Nonbonded interactions: 29031
  Sorted by model distance:
  nonbonded model="   5" pdb=" H   LYS A  79 "
            model="   5" pdb=" HB  THR A  92 "
     model   vdw
     1.477 2.270
  nonbonded model="   5" pdb=" H   THR A  92 "
            model="   5" pdb=" H   LEU A  99 "
     model   vdw
     1.719 2.100
  nonbonded model="   5" pdb=" H   ILE A  77 "
            model="   5" pdb=" H   ILE A  78 "
     model   vdw
     1.771 2.100
  nonbonded model="   5" pdb=" O   LEU A  61 "
            model="   5" pdb=" HG  SER A  65 "
     model   vdw
     1.804 1.850
  nonbonded model="   5" pdb=" HG  SER A  17 "
            model="   5" pdb=" OD2 ASP A  74 "
     model   vdw
     1.839 1.850
  ... (remaining 29026 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.24, per 1000 atoms: 0.56
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.665, 50.702, 44.279, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.70
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  LEU A   2 "
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  PRO A  52 "
        model="   1" pdb=" CB  ILE A  78 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CB  TYR A  89 "
        model="   1" pdb=" CB  LEU A 119 "
        model="   1" pdb=" CB  GLU A 133 "
        model="   1" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  246

  Time building geometry restraints manager: 1.82 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.58
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.66 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 49
        1.23 -     1.42: 426
        1.42 -     1.62: 656
        1.62 -     1.81: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   1" pdb=" N   GLY A  80 "
       model="   1" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.560 -0.109 1.60e-02 3.91e+03 4.66e+01
  bond model="   1" pdb=" N   LYS A  79 "
       model="   1" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.587 -0.129 1.90e-02 2.77e+03 4.64e+01
  bond model="   1" pdb=" CA  ILE A  78 "
       model="   1" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.643 -0.118 2.10e-02 2.27e+03 3.16e+01
  bond model="   1" pdb=" CA  LYS A  79 "
       model="   1" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.604 -0.079 2.10e-02 2.27e+03 1.42e+01
  bond model="   1" pdb=" CA  ASP A  88 "
       model="   1" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.594 -0.069 2.10e-02 2.27e+03 1.08e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       82.88 -    94.22: 5
       94.22 -   105.55: 133
      105.55 -   116.88: 2887
      116.88 -   128.22: 1033
      128.22 -   139.55: 21
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   1" pdb=" C   ILE A  78 "
        model="   1" pdb=" CA  ILE A  78 "
        model="   1" pdb=" CB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     111.60  133.32  -21.72 2.00e+00 2.50e-01 1.18e+02
  angle model="   1" pdb=" CB  ARG A 129 "
        model="   1" pdb=" CG  ARG A 129 "
        model="   1" pdb=" CD  ARG A 129 "
      ideal   model   delta    sigma   weight residual
     111.30  134.52  -23.22 2.30e+00 1.89e-01 1.02e+02
  angle model="   1" pdb=" C   LYS A  79 "
        model="   1" pdb=" N   GLY A  80 "
        model="   1" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  139.55  -17.85 1.80e+00 3.09e-01 9.83e+01
  angle model="   1" pdb=" C   THR A  92 "
        model="   1" pdb=" N   LEU A  93 "
        model="   1" pdb=" CA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     121.70  105.56   16.14 1.80e+00 3.09e-01 8.04e+01
  angle model="   1" pdb=" C   ILE A  78 "
        model="   1" pdb=" CA  ILE A  78 "
        model="   1" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   82.88   26.12 3.00e+00 1.11e-01 7.58e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.82: 928
       19.82 -    39.64: 59
       39.64 -    59.46: 18
       59.46 -    79.27: 6
       79.27 -    99.09: 4
  Dihedral angle restraints: 1015
    sinusoidal: 562
      harmonic: 453
  Sorted by residual:
  dihedral model="   1" pdb=" CA  LEU A  93 "
           model="   1" pdb=" C   LEU A  93 "
           model="   1" pdb=" N   GLY A  94 "
           model="   1" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -80.91  -99.09     0      5.00e+00 4.00e-02 3.93e+02
  dihedral model="   1" pdb=" CA  GLU A  75 "
           model="   1" pdb=" C   GLU A  75 "
           model="   1" pdb=" N   SER A  76 "
           model="   1" pdb=" CA  SER A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   83.52   96.48     0      5.00e+00 4.00e-02 3.72e+02
  dihedral model="   1" pdb=" CA  THR A  92 "
           model="   1" pdb=" C   THR A  92 "
           model="   1" pdb=" N   LEU A  93 "
           model="   1" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   88.94   91.06     0      5.00e+00 4.00e-02 3.32e+02
  ... (remaining 1012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.100: 164
       1.100 -    2.198: 1
       2.198 -    3.297: 0
       3.297 -    4.396: 2
       4.396 -    5.495: 9
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CB  ILE A  78 "
            model="   1" pdb=" CA  ILE A  78 "
            model="   1" pdb=" CG1 ILE A  78 "
            model="   1" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.85    5.49 2.00e-01 2.50e+01 7.55e+02
  chirality model="   1" pdb=" CA  LYS A  79 "
            model="   1" pdb=" N   LYS A  79 "
            model="   1" pdb=" C   LYS A  79 "
            model="   1" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.86    5.37 2.00e-01 2.50e+01 7.22e+02
  chirality model="   1" pdb=" CA  PRO A  52 "
            model="   1" pdb=" N   PRO A  52 "
            model="   1" pdb=" C   PRO A  52 "
            model="   1" pdb=" CB  PRO A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72   -2.46    5.18 2.00e-01 2.50e+01 6.71e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  89 "    0.301 2.00e-02 2.50e+03   1.16e-01 4.03e+02
        model="   1" pdb=" CG  TYR A  89 "   -0.040 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  89 "   -0.076 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  89 "   -0.064 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  89 "   -0.008 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  89 "   -0.021 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  89 "    0.039 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  89 "    0.151 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  89 "   -0.146 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  89 "   -0.109 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  89 "    0.006 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  89 "   -0.032 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  50 "    0.143 2.00e-02 2.50e+03   5.59e-02 9.37e+01
        model="   1" pdb=" CG  TYR A  50 "   -0.031 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  50 "   -0.032 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  50 "   -0.033 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  50 "    0.090 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  50 "   -0.047 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  50 "   -0.049 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  PHE A  15 "    0.103 2.00e-02 2.50e+03   4.17e-02 5.22e+01
        model="   1" pdb=" CG  PHE A  15 "   -0.022 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 PHE A  15 "   -0.033 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 PHE A  15 "   -0.019 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 PHE A  15 "    0.006 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 PHE A  15 "   -0.009 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  PHE A  15 "    0.018 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 PHE A  15 "   -0.067 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 PHE A  15 "   -0.023 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 PHE A  15 "    0.024 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 PHE A  15 "   -0.021 2.00e-02 2.50e+03
        model="   1" pdb=" HZ  PHE A  15 "    0.044 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.33: 517
        2.33 -     2.90: 5298
        2.90 -     3.46: 5941
        3.46 -     4.03: 7598
        4.03 -     4.60: 11270
  Nonbonded interactions: 30624
  Sorted by model distance:
  nonbonded model="   1" pdb=" H   ASP A  95 "
            model="   1" pdb=" H   GLY A  96 "
     model   vdw
     1.760 2.100
  nonbonded model="   1" pdb=" O   LEU A  61 "
            model="   1" pdb=" HG  SER A  65 "
     model   vdw
     1.798 1.850
  nonbonded model="   1" pdb=" HB  ILE A  86 "
            model="   1" pdb=" H   TYR A  89 "
     model   vdw
     1.819 2.270
  nonbonded model="   1" pdb=" HA  ILE A  78 "
            model="   1" pdb=" HA3 GLY A  80 "
     model   vdw
     1.819 2.440
  nonbonded model="   1" pdb=" H   GLY A  80 "
            model="   1" pdb=" O   LEU A  93 "
     model   vdw
     1.822 1.850
  ... (remaining 30619 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 70
        1.23 -     1.42: 402
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" CZ  ARG A  21 "
       model="  11" pdb=" NH1 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.323  1.286  0.037 1.40e-02 5.10e+03 7.14e+00
  bond model="  11" pdb=" CD2 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.02e+00
  bond model="  11" pdb=" CZ  ARG A  58 "
       model="  11" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.68e+00
  bond model="  11" pdb=" ND1 HIS A 136 "
       model="  11" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.42e+00
  bond model="  11" pdb=" CZ  ARG A  21 "
       model="  11" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 5.15e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.10 -   106.15: 129
      106.15 -   112.20: 2489
      112.20 -   118.24: 505
      118.24 -   124.29: 856
      124.29 -   130.34: 100
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" OE1 GLN A  28 "
        model="  11" pdb=" CD  GLN A  28 "
        model="  11" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  117.79    4.81 1.00e+00 1.00e+00 2.31e+01
  angle model="  11" pdb=" CA  TYR A 105 "
        model="  11" pdb=" CB  TYR A 105 "
        model="  11" pdb=" CG  TYR A 105 "
      ideal   model   delta    sigma   weight residual
     113.90  122.12   -8.22 1.80e+00 3.09e-01 2.09e+01
  angle model="  11" pdb=" OE1 GLN A 100 "
        model="  11" pdb=" CD  GLN A 100 "
        model="  11" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.09    4.51 1.00e+00 1.00e+00 2.04e+01
  angle model="  11" pdb=" OE1 GLN A  66 "
        model="  11" pdb=" CD  GLN A  66 "
        model="  11" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.48    4.12 1.00e+00 1.00e+00 1.70e+01
  angle model="  11" pdb=" CB  HIS A  43 "
        model="  11" pdb=" CG  HIS A  43 "
        model="  11" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.66    4.54 1.30e+00 5.92e-01 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 941
       17.85 -    35.70: 63
       35.70 -    53.55: 25
       53.55 -    71.39: 3
       71.39 -    89.24: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  11" pdb=" CA  GLU A 133 "
           model="  11" pdb=" C   GLU A 133 "
           model="  11" pdb=" N   HIS A 134 "
           model="  11" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.07  -30.93     0      5.00e+00 4.00e-02 3.83e+01
  dihedral model="  11" pdb=" C   ILE A 108 "
           model="  11" pdb=" N   ILE A 108 "
           model="  11" pdb=" CA  ILE A 108 "
           model="  11" pdb=" CB  ILE A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.76   11.76     0      2.50e+00 1.60e-01 2.21e+01
  dihedral model="  11" pdb=" CA  ALA A 115 "
           model="  11" pdb=" C   ALA A 115 "
           model="  11" pdb=" N   ASP A 116 "
           model="  11" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.14   22.86     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 93
       0.061 -    0.122: 46
       0.122 -    0.184: 29
       0.184 -    0.245: 7
       0.245 -    0.306: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  ILE A 108 "
            model="  11" pdb=" N   ILE A 108 "
            model="  11" pdb=" C   ILE A 108 "
            model="  11" pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.13    0.31 2.00e-01 2.50e+01 2.34e+00
  chirality model="  11" pdb=" CB  THR A  82 "
            model="  11" pdb=" CA  THR A  82 "
            model="  11" pdb=" OG1 THR A  82 "
            model="  11" pdb=" CG2 THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality model="  11" pdb=" CA  ASP A 103 "
            model="  11" pdb=" N   ASP A 103 "
            model="  11" pdb=" C   ASP A 103 "
            model="  11" pdb=" CB  ASP A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A 105 "   -0.258 2.00e-02 2.50e+03   1.04e-01 3.25e+02
        model="  11" pdb=" CG  TYR A 105 "    0.068 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A 105 "    0.045 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A 105 "    0.073 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A 105 "    0.040 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A 105 "    0.012 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A 105 "   -0.005 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A 105 "   -0.174 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A 105 "    0.033 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A 105 "    0.118 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A 105 "    0.065 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A 105 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  50 "    0.160 2.00e-02 2.50e+03   6.61e-02 1.31e+02
        model="  11" pdb=" CG  TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  50 "   -0.044 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  50 "    0.109 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  50 "   -0.036 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  50 "   -0.086 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  50 "   -0.050 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  50 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  89 "   -0.155 2.00e-02 2.50e+03   6.01e-02 1.08e+02
        model="  11" pdb=" CG  TYR A  89 "    0.047 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  89 "    0.049 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  89 "    0.030 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  89 "   -0.011 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  89 "    0.009 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  89 "   -0.023 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  89 "   -0.044 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  89 "    0.090 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  89 "    0.033 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  89 "   -0.041 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  89 "    0.017 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 145
        2.20 -     2.80: 4232
        2.80 -     3.40: 5787
        3.40 -     4.00: 6749
        4.00 -     4.60: 10058
  Nonbonded interactions: 26971
  Sorted by model distance:
  nonbonded model="  11" pdb="HD11 ILE A  71 "
            model="  11" pdb=" H   GLY A  87 "
     model   vdw
     1.598 2.270
  nonbonded model="  11" pdb=" OD2 ASP A  36 "
            model="  11" pdb=" HZ1 LYS A  40 "
     model   vdw
     1.704 1.850
  nonbonded model="  11" pdb=" HZ1 LYS A  10 "
            model="  11" pdb=" OD1 ASP A  23 "
     model   vdw
     1.753 1.850
  nonbonded model="  11" pdb=" OE2 GLU A  16 "
            model="  11" pdb=" HZ2 LYS A  19 "
     model   vdw
     1.793 1.850
  nonbonded model="  11" pdb="HH22 ARG A  21 "
            model="  11" pdb=" HB3 ASN A  72 "
     model   vdw
     1.811 2.270
  ... (remaining 26966 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (52.204, 42.435, 69.573, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CB  ILE A  78 "
        model="   6" pdb=" CB  LEU A 119 "
        model="   6" pdb=" CB  ALA A 124 "
        model="   6" pdb=" CB  VAL A 126 "
        model="   6" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   8" pdb=" N   MET A   1 "
       model="   8" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.45e+00
  bond model="   8" pdb=" CZ  ARG A 127 "
       model="   8" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 7.02e-02
  bond model="   8" pdb=" NE  ARG A 129 "
       model="   8" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 6.92e-02
  bond model="   8" pdb=" CZ  ARG A  58 "
       model="   8" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.327 -0.004 1.40e-02 5.10e+03 6.35e-02
  bond model="   8" pdb=" CZ  ARG A 129 "
       model="   8" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.33e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.89 -   106.88: 64
      106.88 -   112.87: 2721
      112.87 -   118.86: 426
      118.86 -   124.86: 824
      124.86 -   130.85: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   8" pdb=" CB  PRO A  52 "
        model="   8" pdb=" CA  PRO A  52 "
        model="   8" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.60e+00
  angle model="   8" pdb=" CB  PRO A 102 "
        model="   8" pdb=" CA  PRO A 102 "
        model="   8" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   8" pdb=" CB  PRO A   6 "
        model="   8" pdb=" CA  PRO A   6 "
        model="   8" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   8" pdb=" CB  PRO A 117 "
        model="   8" pdb=" CA  PRO A 117 "
        model="   8" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   8" pdb=" CB  PRO A 114 "
        model="   8" pdb=" CA  PRO A 114 "
        model="   8" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.08: 869
       16.08 -    32.16: 81
       32.16 -    48.25: 49
       48.25 -    64.33: 27
       64.33 -    80.41: 6
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   8" pdb=" CB  ARG A  58 "
           model="   8" pdb=" CG  ARG A  58 "
           model="   8" pdb=" CD  ARG A  58 "
           model="   8" pdb=" NE  ARG A  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.33  -59.67     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   8" pdb=" CA  MET A 128 "
           model="   8" pdb=" CB  MET A 128 "
           model="   8" pdb=" CG  MET A 128 "
           model="   8" pdb=" SD  MET A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.52  -59.52     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   8" pdb=" CA  ARG A 129 "
           model="   8" pdb=" CB  ARG A 129 "
           model="   8" pdb=" CG  ARG A 129 "
           model="   8" pdb=" CD  ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.69   59.31     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 100
       0.019 -    0.038: 54
       0.038 -    0.057: 3
       0.057 -    0.075: 0
       0.075 -    0.094: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  ILE A  78 "
            model="   8" pdb=" N   ILE A  78 "
            model="   8" pdb=" C   ILE A  78 "
            model="   8" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.21e-01
  chirality model="   8" pdb=" CA  ILE A  37 "
            model="   8" pdb=" N   ILE A  37 "
            model="   8" pdb=" C   ILE A  37 "
            model="   8" pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.21e-01
  chirality model="   8" pdb=" CA  ILE A 122 "
            model="   8" pdb=" N   ILE A 122 "
            model="   8" pdb=" C   ILE A 122 "
            model="   8" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.16e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  PHE A  45 "   -0.000 2.00e-02 2.50e+03   1.39e-03 5.78e-02
        model="   8" pdb=" CG  PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 PHE A  45 "    0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HZ  PHE A  45 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  89 "   -0.001 2.00e-02 2.50e+03   1.21e-03 4.41e-02
        model="   8" pdb=" CG  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  89 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  12 "   -0.001 2.00e-02 2.50e+03   9.75e-04 2.85e-02
        model="   8" pdb=" CG  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.09: 103
        2.09 -     2.72: 4029
        2.72 -     3.35: 6086
        3.35 -     3.97: 7258
        3.97 -     4.60: 11036
  Nonbonded interactions: 28512
  Sorted by model distance:
  nonbonded model="   8" pdb="HG12 VAL A  41 "
            model="   8" pdb="HG22 VAL A 112 "
     model   vdw
     1.468 2.440
  nonbonded model="   8" pdb="HG23 ILE A  37 "
            model="   8" pdb="HD13 ILE A 108 "
     model   vdw
     1.653 2.440
  nonbonded model="   8" pdb="HD11 LEU A  93 "
            model="   8" pdb="HD13 LEU A  99 "
     model   vdw
     1.693 2.440
  nonbonded model="   8" pdb="HD23 LEU A   9 "
            model="   8" pdb="HD22 LEU A  26 "
     model   vdw
     1.706 2.440
  nonbonded model="   8" pdb="HD11 LEU A   2 "
            model="   8" pdb="HG22 ILE A  30 "
     model   vdw
     1.726 2.440
  ... (remaining 28507 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 68
        1.23 -     1.42: 404
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  10" pdb=" CD2 HIS A 138 "
       model="  10" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.410 -0.036 1.10e-02 8.26e+03 1.08e+01
  bond model="  10" pdb=" CE1 HIS A 136 "
       model="  10" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.17e+00
  bond model="  10" pdb=" CD2 HIS A 139 "
       model="  10" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 8.15e+00
  bond model="  10" pdb=" CE1 HIS A 138 "
       model="  10" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.96e+00
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.44e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.62 -   105.97: 128
      105.97 -   112.32: 2514
      112.32 -   118.67: 517
      118.67 -   125.02: 869
      125.02 -   131.37: 51
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  10" pdb=" C   ALA A 124 "
        model="  10" pdb=" N   LYS A 125 "
        model="  10" pdb=" CA  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     121.70  131.37   -9.67 1.80e+00 3.09e-01 2.88e+01
  angle model="  10" pdb=" OE1 GLN A  66 "
        model="  10" pdb=" CD  GLN A  66 "
        model="  10" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.16    4.44 1.00e+00 1.00e+00 1.97e+01
  angle model="  10" pdb=" OE1 GLN A 100 "
        model="  10" pdb=" CD  GLN A 100 "
        model="  10" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.51    4.09 1.00e+00 1.00e+00 1.67e+01
  angle model="  10" pdb=" N   LYS A 125 "
        model="  10" pdb=" CA  LYS A 125 "
        model="  10" pdb=" C   LYS A 125 "
      ideal   model   delta    sigma   weight residual
     111.00  122.06  -11.06 2.80e+00 1.28e-01 1.56e+01
  angle model="  10" pdb=" C   ASP A 103 "
        model="  10" pdb=" N   VAL A 104 "
        model="  10" pdb=" CA  VAL A 104 "
      ideal   model   delta    sigma   weight residual
     121.70  128.70   -7.00 1.80e+00 3.09e-01 1.51e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.48: 933
       14.48 -    28.96: 73
       28.96 -    43.45: 20
       43.45 -    57.93: 4
       57.93 -    72.41: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  10" pdb=" C   ILE A 108 "
           model="  10" pdb=" N   ILE A 108 "
           model="  10" pdb=" CA  ILE A 108 "
           model="  10" pdb=" CB  ILE A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.21   11.21     0      2.50e+00 1.60e-01 2.01e+01
  dihedral model="  10" pdb=" C   VAL A 104 "
           model="  10" pdb=" N   VAL A 104 "
           model="  10" pdb=" CA  VAL A 104 "
           model="  10" pdb=" CB  VAL A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.12   11.12     0      2.50e+00 1.60e-01 1.98e+01
  dihedral model="  10" pdb=" CA  LYS A  85 "
           model="  10" pdb=" C   LYS A  85 "
           model="  10" pdb=" N   ILE A  86 "
           model="  10" pdb=" CA  ILE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.68   21.32     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 98
       0.071 -    0.142: 60
       0.142 -    0.213: 11
       0.213 -    0.284: 3
       0.284 -    0.355: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CA  GLU A 123 "
            model="  10" pdb=" N   GLU A 123 "
            model="  10" pdb=" C   GLU A 123 "
            model="  10" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.14e+00
  chirality model="  10" pdb=" CA  ILE A 108 "
            model="  10" pdb=" N   ILE A 108 "
            model="  10" pdb=" C   ILE A 108 "
            model="  10" pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.11    0.33 2.00e-01 2.50e+01 2.68e+00
  chirality model="  10" pdb=" CA  VAL A 104 "
            model="  10" pdb=" N   VAL A 104 "
            model="  10" pdb=" C   VAL A 104 "
            model="  10" pdb=" CB  VAL A 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.13    0.32 2.00e-01 2.50e+01 2.49e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  89 "   -0.320 2.00e-02 2.50e+03   1.21e-01 4.39e+02
        model="  10" pdb=" CG  TYR A  89 "    0.052 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  89 "    0.077 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  89 "    0.075 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  89 "    0.009 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  89 "   -0.064 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  89 "   -0.132 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  89 "    0.138 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  89 "    0.135 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  89 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  81 "   -0.198 2.00e-02 2.50e+03   7.97e-02 1.91e+02
        model="  10" pdb=" CG  TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  81 "    0.043 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  81 "    0.045 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  81 "    0.017 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  81 "    0.015 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  81 "   -0.125 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  81 "    0.083 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  81 "    0.090 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  81 "    0.027 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  81 "    0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  HIS A 137 "    0.116 2.00e-02 2.50e+03   7.00e-02 9.80e+01
        model="  10" pdb=" CG  HIS A 137 "   -0.092 2.00e-02 2.50e+03
        model="  10" pdb=" ND1 HIS A 137 "   -0.086 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 HIS A 137 "   -0.021 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 HIS A 137 "    0.012 2.00e-02 2.50e+03
        model="  10" pdb=" NE2 HIS A 137 "    0.083 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 HIS A 137 "   -0.039 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 HIS A 137 "    0.029 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 149
        2.22 -     2.81: 4451
        2.81 -     3.41: 5877
        3.41 -     4.00: 6964
        4.00 -     4.60: 10372
  Nonbonded interactions: 27813
  Sorted by model distance:
  nonbonded model="  10" pdb=" HB2 GLU A  32 "
            model="  10" pdb="HG21 ILE A  86 "
     model   vdw
     1.621 2.440
  nonbonded model="  10" pdb=" OD2 ASP A  36 "
            model="  10" pdb=" HZ2 LYS A  40 "
     model   vdw
     1.685 1.850
  nonbonded model="  10" pdb=" HZ1 LYS A  10 "
            model="  10" pdb=" OD1 ASP A  23 "
     model   vdw
     1.766 1.850
  nonbonded model="  10" pdb=" O   ARG A 127 "
            model="  10" pdb=" HG  SER A 130 "
     model   vdw
     1.827 1.850
  nonbonded model="  10" pdb=" OD1 ASP A  74 "
            model="  10" pdb=" HG  SER A  76 "
     model   vdw
     1.839 1.850
  ... (remaining 27808 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 61
        1.23 -     1.43: 415
        1.43 -     1.62: 656
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   6" pdb=" C   VAL A 126 "
       model="   6" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.258  0.071 1.40e-02 5.10e+03 2.60e+01
  bond model="   6" pdb=" CA  GLY A 121 "
       model="   6" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.594 -0.078 1.80e-02 3.09e+03 1.90e+01
  bond model="   6" pdb=" N   ILE A 122 "
       model="   6" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.536 -0.078 1.90e-02 2.77e+03 1.70e+01
  bond model="   6" pdb=" N   GLY A  80 "
       model="   6" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.514 -0.063 1.60e-02 3.91e+03 1.57e+01
  bond model="   6" pdb=" CA  ASP A  88 "
       model="   6" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.598 -0.073 2.10e-02 2.27e+03 1.19e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       52.51 -    69.21: 1
       69.21 -    85.91: 0
       85.91 -   102.61: 42
      102.61 -   119.31: 3153
      119.31 -   136.01: 883
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   6" pdb=" N   TYR A  81 "
        model="   6" pdb=" CA  TYR A  81 "
        model="   6" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     110.00   52.51   57.49 3.00e+00 1.11e-01 3.67e+02
  angle model="   6" pdb=" CA  TYR A  81 "
        model="   6" pdb=" CB  TYR A  81 "
        model="   6" pdb=" CG  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     113.90  132.37  -18.47 1.80e+00 3.09e-01 1.05e+02
  angle model="   6" pdb=" C   TYR A  89 "
        model="   6" pdb=" N   SER A  90 "
        model="   6" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  103.39   18.31 1.80e+00 3.09e-01 1.03e+02
  angle model="   6" pdb=" CA  VAL A 126 "
        model="   6" pdb=" C   VAL A 126 "
        model="   6" pdb=" N   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     116.20   97.76   18.44 2.00e+00 2.50e-01 8.50e+01
  angle model="   6" pdb=" C   ASP A  88 "
        model="   6" pdb=" N   TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     121.70  136.01  -14.31 1.80e+00 3.09e-01 6.32e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.72: 923
       20.72 -    41.43: 62
       41.43 -    62.15: 24
       62.15 -    82.86: 5
       82.86 -   103.58: 7
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   6" pdb=" C   TYR A  81 "
           model="   6" pdb=" N   TYR A  81 "
           model="   6" pdb=" CA  TYR A  81 "
           model="   6" pdb=" CB  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -176.99   54.39     0      2.50e+00 1.60e-01 4.73e+02
  dihedral model="   6" pdb=" N   TYR A  81 "
           model="   6" pdb=" C   TYR A  81 "
           model="   6" pdb=" CA  TYR A  81 "
           model="   6" pdb=" CB  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  177.11  -54.31     0      2.50e+00 1.60e-01 4.72e+02
  dihedral model="   6" pdb=" CA  VAL A 126 "
           model="   6" pdb=" C   VAL A 126 "
           model="   6" pdb=" N   ARG A 127 "
           model="   6" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -76.42 -103.58     0      5.00e+00 4.00e-02 4.29e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.068: 167
       1.068 -    2.135: 1
       2.135 -    3.201: 1
       3.201 -    4.268: 2
       4.268 -    5.335: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CA  ALA A 124 "
            model="   6" pdb=" N   ALA A 124 "
            model="   6" pdb=" C   ALA A 124 "
            model="   6" pdb=" CB  ALA A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48   -2.85    5.33 2.00e-01 2.50e+01 7.12e+02
  chirality model="   6" pdb=" CB  ILE A  78 "
            model="   6" pdb=" CA  ILE A  78 "
            model="   6" pdb=" CG1 ILE A  78 "
            model="   6" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.46    5.10 2.00e-01 2.50e+01 6.51e+02
  chirality model="   6" pdb=" CA  HIS A 139 "
            model="   6" pdb=" N   HIS A 139 "
            model="   6" pdb=" C   HIS A 139 "
            model="   6" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.50    5.02 2.00e-01 2.50e+01 6.29e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  81 "   -0.192 2.00e-02 2.50e+03   1.09e-01 3.55e+02
        model="   6" pdb=" CG  TYR A  81 "   -0.078 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  81 "    0.066 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  81 "   -0.017 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  81 "    0.043 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  81 "   -0.062 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  81 "   -0.131 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  81 "    0.221 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  81 "    0.046 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  81 "   -0.042 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  81 "    0.137 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  PHE A  67 "    0.117 2.00e-02 2.50e+03   5.93e-02 1.05e+02
        model="   6" pdb=" CG  PHE A  67 "   -0.022 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 PHE A  67 "   -0.012 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 PHE A  67 "   -0.041 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 PHE A  67 "   -0.028 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  PHE A  67 "    0.037 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 PHE A  67 "    0.004 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 PHE A  67 "   -0.081 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 PHE A  67 "   -0.082 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 PHE A  67 "    0.003 2.00e-02 2.50e+03
        model="   6" pdb=" HZ  PHE A  67 "    0.105 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A 111 "    0.119 2.00e-02 2.50e+03   4.69e-02 6.60e+01
        model="   6" pdb=" CG  TYR A 111 "   -0.029 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A 111 "   -0.028 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A 111 "   -0.027 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A 111 "    0.079 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A 111 "   -0.036 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.26: 296
        2.26 -     2.84: 4882
        2.84 -     3.43: 6093
        3.43 -     4.01: 7792
        4.01 -     4.60: 11273
  Nonbonded interactions: 30336
  Sorted by model distance:
  nonbonded model="   6" pdb="HG23 ILE A  77 "
            model="   6" pdb=" H   GLY A  94 "
     model   vdw
     1.673 2.270
  nonbonded model="   6" pdb=" HA  ALA A 124 "
            model="   6" pdb=" HB  VAL A 126 "
     model   vdw
     1.724 2.440
  nonbonded model="   6" pdb=" H   TYR A  81 "
            model="   6" pdb=" HA  TYR A  81 "
     model   vdw
     1.735 1.816
  nonbonded model="   6" pdb=" HA  ALA A 124 "
            model="   6" pdb=" H   VAL A 126 "
     model   vdw
     1.758 2.270
  nonbonded model="   6" pdb=" H   TYR A  89 "
            model="   6" pdb=" HA  TYR A  89 "
     model   vdw
     1.784 1.816
  ... (remaining 30331 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.041, 48.665, 47.464, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   0" pdb=" CB  ILE A  51 "
        model="   0" pdb=" CB  ILE A  78 "
        model="   0" pdb=" CB  LYS A  79 "
        model="   0" pdb=" CB  LEU A 119 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 1.04 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  11" pdb=" CB  LYS A  85 "
        model="  11" pdb=" CB  LEU A 132 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 1.06 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 51
        1.23 -     1.43: 423
        1.43 -     1.62: 658
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CA  THR A  92 "
       model="   0" pdb=" C   THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.525  1.452  0.073 2.10e-02 2.27e+03 1.22e+01
  bond model="   0" pdb=" N   LEU A 119 "
       model="   0" pdb=" CA  LEU A 119 "
    ideal  model  delta    sigma   weight residual
    1.458  1.521 -0.063 1.90e-02 2.77e+03 1.09e+01
  bond model="   0" pdb=" N   TYR A  89 "
       model="   0" pdb=" CA  TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.517 -0.059 1.90e-02 2.77e+03 9.67e+00
  bond model="   0" pdb=" CA  ILE A  77 "
       model="   0" pdb=" C   ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.525  1.589 -0.064 2.10e-02 2.27e+03 9.22e+00
  bond model="   0" pdb=" N   LEU A  93 "
       model="   0" pdb=" CA  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.458  1.403  0.055 1.90e-02 2.77e+03 8.33e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       92.74 -   101.20: 14
      101.20 -   109.65: 2011
      109.65 -   118.10: 1092
      118.10 -   126.56: 936
      126.56 -   135.01: 26
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
        model="   0" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.10   93.15   16.95 1.90e+00 2.77e-01 7.95e+01
  angle model="   0" pdb=" C   ILE A  78 "
        model="   0" pdb=" N   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  135.01  -13.31 1.80e+00 3.09e-01 5.47e+01
  angle model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     121.70  134.79  -13.09 1.80e+00 3.09e-01 5.29e+01
  angle model="   0" pdb=" C   SER A  76 "
        model="   0" pdb=" N   ILE A  77 "
        model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     121.70  133.69  -11.99 1.80e+00 3.09e-01 4.44e+01
  angle model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" N   PRO A  52 "
        model="   0" pdb=" CD  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     112.00  102.86    9.14 1.40e+00 5.10e-01 4.26e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 918
       17.96 -    35.91: 75
       35.91 -    53.87: 17
       53.87 -    71.82: 14
       71.82 -    89.78: 1
  Dihedral angle restraints: 1025
    sinusoidal: 562
      harmonic: 463
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -112.39  -67.61     0      5.00e+00 4.00e-02 1.83e+02
  dihedral model="   0" pdb=" CA  ILE A  77 "
           model="   0" pdb=" C   ILE A  77 "
           model="   0" pdb=" N   ILE A  78 "
           model="   0" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -113.29  -66.71     0      5.00e+00 4.00e-02 1.78e+02
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -113.74  -66.26     0      5.00e+00 4.00e-02 1.76e+02
  ... (remaining 1022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.130: 170
       1.130 -    2.258: 0
       2.258 -    3.386: 0
       3.386 -    4.514: 1
       4.514 -    5.642: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  79 "
            model="   0" pdb=" N   LYS A  79 "
            model="   0" pdb=" C   LYS A  79 "
            model="   0" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.13    5.64 2.00e-01 2.50e+01 7.96e+02
  chirality model="   0" pdb=" CB  ILE A  78 "
            model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" CG1 ILE A  78 "
            model="   0" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.67    5.32 2.00e-01 2.50e+01 7.07e+02
  chirality model="   0" pdb=" CA  LEU A 119 "
            model="   0" pdb=" N   LEU A 119 "
            model="   0" pdb=" C   LEU A 119 "
            model="   0" pdb=" CB  LEU A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.64    5.16 2.00e-01 2.50e+01 6.64e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.156 2.00e-02 2.50e+03   7.01e-02 1.48e+02
        model="   0" pdb=" CG  TYR A  89 "    0.078 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.112 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.102 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.119 2.00e-02 2.50e+03   5.15e-02 7.96e+01
        model="   0" pdb=" CG  TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.102 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.039 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.117 2.00e-02 2.50e+03   4.47e-02 6.01e+01
        model="   0" pdb=" CG  TYR A  50 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 132
        2.16 -     2.77: 4108
        2.77 -     3.38: 6583
        3.38 -     3.99: 7870
        3.99 -     4.60: 11875
  Nonbonded interactions: 30568
  Sorted by model distance:
  nonbonded model="   0" pdb=" H   THR A  92 "
            model="   0" pdb=" HB2 LEU A  99 "
     model   vdw
     1.546 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.740 1.850
  nonbonded model="   0" pdb="HG22 ILE A  77 "
            model="   0" pdb=" H   ILE A  78 "
     model   vdw
     1.752 2.270
  nonbonded model="   0" pdb=" H   GLY A  80 "
            model="   0" pdb="HD22 LEU A  93 "
     model   vdw
     1.779 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.786 1.850
  ... (remaining 30563 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  11" pdb=" CB  SER A  98 "
  Number of C-beta restraints generated:  262

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 90
        1.23 -     1.43: 382
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" CD2 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.32e+00
  bond model="  11" pdb=" CZ  ARG A  58 "
       model="  11" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.27e+00
  bond model="  11" pdb=" CZ  ARG A  21 "
       model="  11" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.70e+00
  bond model="  11" pdb=" ND1 HIS A 138 "
       model="  11" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.03e+00
  bond model="  11" pdb=" CD2 HIS A 137 "
       model="  11" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.399 -0.025 1.10e-02 8.26e+03 5.37e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.04 -   105.19: 68
      105.19 -   111.35: 2387
      111.35 -   117.50: 622
      117.50 -   123.66: 865
      123.66 -   129.82: 137
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" CA  ASP A  95 "
        model="  11" pdb=" CB  ASP A  95 "
        model="  11" pdb=" CG  ASP A  95 "
      ideal   model   delta    sigma   weight residual
     112.60  107.86    4.74 1.00e+00 1.00e+00 2.24e+01
  angle model="  11" pdb=" CB  HIS A 138 "
        model="  11" pdb=" CG  HIS A 138 "
        model="  11" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  125.16    6.04 1.30e+00 5.92e-01 2.16e+01
  angle model="  11" pdb=" C   ILE A 131 "
        model="  11" pdb=" N   LEU A 132 "
        model="  11" pdb=" CA  LEU A 132 "
      ideal   model   delta    sigma   weight residual
     121.70  129.82   -8.12 1.80e+00 3.09e-01 2.03e+01
  angle model="  11" pdb=" N   LEU A 132 "
        model="  11" pdb=" CA  LEU A 132 "
        model="  11" pdb=" CB  LEU A 132 "
      ideal   model   delta    sigma   weight residual
     110.50  117.94   -7.44 1.70e+00 3.46e-01 1.92e+01
  angle model="  11" pdb=" C   LYS A  85 "
        model="  11" pdb=" N   ILE A  86 "
        model="  11" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  129.07   -7.37 1.80e+00 3.09e-01 1.68e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.17: 951
       18.17 -    36.35: 51
       36.35 -    54.52: 12
       54.52 -    72.70: 6
       72.70 -    90.87: 9
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  11" pdb=" CA  ILE A  51 "
           model="  11" pdb=" C   ILE A  51 "
           model="  11" pdb=" N   PRO A  52 "
           model="  11" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -21.08   21.08     0      5.00e+00 4.00e-02 1.78e+01
  dihedral model="  11" pdb=" CA  GLY A  94 "
           model="  11" pdb=" C   GLY A  94 "
           model="  11" pdb=" N   ASP A  95 "
           model="  11" pdb=" CA  ASP A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.30   20.70     0      5.00e+00 4.00e-02 1.71e+01
  dihedral model="  11" pdb=" C   LYS A 101 "
           model="  11" pdb=" N   LYS A 101 "
           model="  11" pdb=" CA  LYS A 101 "
           model="  11" pdb=" CB  LYS A 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.78   10.18     0      2.50e+00 1.60e-01 1.66e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.911: 174
       0.911 -    1.823: 0
       1.823 -    2.734: 0
       2.734 -    3.645: 0
       3.645 -    4.557: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  LYS A  85 "
            model="  11" pdb=" N   LYS A  85 "
            model="  11" pdb=" C   LYS A  85 "
            model="  11" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.05    4.56 2.00e-01 2.50e+01 5.19e+02
  chirality model="  11" pdb=" CA  LEU A 132 "
            model="  11" pdb=" N   LEU A 132 "
            model="  11" pdb=" C   LEU A 132 "
            model="  11" pdb=" CB  LEU A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.74    4.25 2.00e-01 2.50e+01 4.51e+02
  chirality model="  11" pdb=" CA  LYS A 101 "
            model="  11" pdb=" N   LYS A 101 "
            model="  11" pdb=" C   LYS A 101 "
            model="  11" pdb=" CB  LYS A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.97e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  68 "   -0.181 2.00e-02 2.50e+03   8.80e-02 2.32e+02
        model="  11" pdb=" CG  TYR A  68 "    0.009 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  68 "    0.030 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  68 "    0.040 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  68 "    0.043 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  68 "    0.033 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  68 "    0.003 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  68 "   -0.202 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  68 "    0.035 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  68 "    0.064 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  68 "    0.078 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  68 "    0.048 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A 105 "    0.155 2.00e-02 2.50e+03   7.25e-02 1.58e+02
        model="  11" pdb=" CG  TYR A 105 "    0.010 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A 105 "   -0.030 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A 105 "   -0.030 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A 105 "   -0.027 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A 105 "   -0.027 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A 105 "    0.012 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A 105 "    0.155 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A 105 "   -0.058 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A 105 "   -0.060 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A 105 "   -0.049 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A 105 "   -0.050 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A 111 "   -0.105 2.00e-02 2.50e+03   4.42e-02 5.87e+01
        model="  11" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A 111 "    0.029 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A 111 "   -0.078 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A 111 "    0.056 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A 111 "    0.034 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.28: 272
        2.28 -     2.86: 4975
        2.86 -     3.44: 5425
        3.44 -     4.02: 7006
        4.02 -     4.60: 10317
  Nonbonded interactions: 27995
  Sorted by model distance:
  nonbonded model="  11" pdb=" H   ILE A  86 "
            model="  11" pdb="HG12 ILE A  86 "
     model   vdw
     1.695 2.270
  nonbonded model="  11" pdb=" OD1 ASP A  44 "
            model="  11" pdb=" HG  SER A  46 "
     model   vdw
     1.813 1.850
  nonbonded model="  11" pdb=" HZ1 LYS A  40 "
            model="  11" pdb=" O   GLN A 100 "
     model   vdw
     1.831 1.850
  nonbonded model="  11" pdb=" OD1 ASP A  36 "
            model="  11" pdb=" HZ2 LYS A  40 "
     model   vdw
     1.833 1.850
  nonbonded model="  11" pdb=" O   LEU A  99 "
            model="  11" pdb=" HZ2 LYS A 101 "
     model   vdw
     1.846 1.850
  ... (remaining 27990 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 60
        1.23 -     1.42: 412
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" CD2 HIS A 138 "
       model="  11" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.98e+00
  bond model="  11" pdb=" CD2 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.85e+00
  bond model="  11" pdb=" CD2 HIS A 134 "
       model="  11" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.52e+00
  bond model="  11" pdb=" CD2 HIS A 135 "
       model="  11" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.16e+00
  bond model="  11" pdb=" CZ  ARG A  21 "
       model="  11" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.11e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       93.67 -   101.38: 7
      101.38 -   109.08: 998
      109.08 -   116.79: 2008
      116.79 -   124.49: 979
      124.49 -   132.20: 87
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" C   LYS A 109 "
        model="  11" pdb=" N   ASP A 110 "
        model="  11" pdb=" CA  ASP A 110 "
      ideal   model   delta    sigma   weight residual
     121.70  132.20  -10.50 1.80e+00 3.09e-01 3.40e+01
  angle model="  11" pdb=" C   LYS A 109 "
        model="  11" pdb=" CA  LYS A 109 "
        model="  11" pdb=" HA  LYS A 109 "
      ideal   model   delta    sigma   weight residual
     109.00   93.67   15.33 3.00e+00 1.11e-01 2.61e+01
  angle model="  11" pdb=" C   ASP A 110 "
        model="  11" pdb=" CA  ASP A 110 "
        model="  11" pdb=" HA  ASP A 110 "
      ideal   model   delta    sigma   weight residual
     109.00   94.11   14.89 3.00e+00 1.11e-01 2.46e+01
  angle model="  11" pdb=" OE1 GLN A  66 "
        model="  11" pdb=" CD  GLN A  66 "
        model="  11" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.80    4.80 1.00e+00 1.00e+00 2.30e+01
  angle model="  11" pdb=" OE1 GLN A  28 "
        model="  11" pdb=" CD  GLN A  28 "
        model="  11" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  117.99    4.61 1.00e+00 1.00e+00 2.13e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 929
       17.42 -    34.84: 68
       34.84 -    52.27: 23
       52.27 -    69.69: 8
       69.69 -    87.11: 3
  Dihedral angle restraints: 1031
    sinusoidal: 562
      harmonic: 469
  Sorted by residual:
  dihedral model="  11" pdb=" C   LYS A 109 "
           model="  11" pdb=" N   LYS A 109 "
           model="  11" pdb=" CA  LYS A 109 "
           model="  11" pdb=" CB  LYS A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -150.39   27.79     0      2.50e+00 1.60e-01 1.24e+02
  dihedral model="  11" pdb=" N   LYS A 109 "
           model="  11" pdb=" C   LYS A 109 "
           model="  11" pdb=" CA  LYS A 109 "
           model="  11" pdb=" CB  LYS A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  149.73  -26.93     0      2.50e+00 1.60e-01 1.16e+02
  dihedral model="  11" pdb=" CA  HIS A 137 "
           model="  11" pdb=" C   HIS A 137 "
           model="  11" pdb=" N   HIS A 138 "
           model="  11" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.97   35.03     0      5.00e+00 4.00e-02 4.91e+01
  ... (remaining 1028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.970: 174
       0.970 -    1.939: 1
       1.939 -    2.908: 0
       2.908 -    3.877: 0
       3.877 -    4.846: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  SER A  98 "
            model="  11" pdb=" N   SER A  98 "
            model="  11" pdb=" C   SER A  98 "
            model="  11" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.34    4.85 2.00e-01 2.50e+01 5.87e+02
  chirality model="  11" pdb=" CA  LYS A 109 "
            model="  11" pdb=" N   LYS A 109 "
            model="  11" pdb=" C   LYS A 109 "
            model="  11" pdb=" CB  LYS A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.35    1.16 2.00e-01 2.50e+01 3.38e+01
  chirality model="  11" pdb=" CA  ASP A 110 "
            model="  11" pdb=" N   ASP A 110 "
            model="  11" pdb=" C   ASP A 110 "
            model="  11" pdb=" CB  ASP A 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.78    0.73 2.00e-01 2.50e+01 1.32e+01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  12 "    0.191 2.00e-02 2.50e+03   8.82e-02 2.33e+02
        model="  11" pdb=" CG  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  12 "   -0.039 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  12 "   -0.036 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  12 "   -0.033 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  12 "   -0.036 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  12 "    0.192 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  12 "   -0.069 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  12 "   -0.060 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  12 "   -0.051 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  12 "   -0.061 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  81 "   -0.209 2.00e-02 2.50e+03   8.24e-02 2.04e+02
        model="  11" pdb=" CG  TYR A  81 "    0.040 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  81 "    0.045 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  81 "    0.050 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  81 "    0.017 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  81 "    0.012 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  81 "   -0.048 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  81 "   -0.124 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  81 "    0.068 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  81 "    0.081 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  81 "    0.041 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  81 "    0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  68 "   -0.140 2.00e-02 2.50e+03   6.70e-02 1.35e+02
        model="  11" pdb=" CG  TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  68 "    0.052 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  68 "    0.011 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  68 "   -0.011 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  68 "    0.028 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  68 "   -0.023 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  68 "   -0.080 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  68 "    0.127 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  68 "    0.007 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  68 "   -0.045 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  68 "    0.073 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 376
        2.30 -     2.87: 5101
        2.87 -     3.45: 5493
        3.45 -     4.02: 7227
        4.02 -     4.60: 10441
  Nonbonded interactions: 28638
  Sorted by model distance:
  nonbonded model="  11" pdb=" HZ1 LYS A  10 "
            model="  11" pdb=" OD1 ASP A  23 "
     model   vdw
     1.721 1.850
  nonbonded model="  11" pdb=" OE1 GLU A  49 "
            model="  11" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.757 1.850
  nonbonded model="  11" pdb=" HG1 THR A  56 "
            model="  11" pdb=" HD2 TYR A 111 "
     model   vdw
     1.765 2.100
  nonbonded model="  11" pdb=" OD1 ASP A  74 "
            model="  11" pdb=" HG  SER A  76 "
     model   vdw
     1.771 1.850
  nonbonded model="  11" pdb=" OE2 GLU A  16 "
            model="  11" pdb=" HZ2 LYS A  19 "
     model   vdw
     1.815 1.850
  ... (remaining 28633 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ILE A  78 "
        model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CB  THR A  92 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 1.04 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 76
        1.23 -     1.43: 399
        1.43 -     1.62: 656
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" CB  THR A  92 "
       model="   2" pdb=" OG1 THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.433  1.337  0.096 1.60e-02 3.91e+03 3.59e+01
  bond model="   2" pdb=" CA  LEU A  93 "
       model="   2" pdb=" CB  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.626 -0.096 2.00e-02 2.50e+03 2.32e+01
  bond model="   2" pdb=" N   GLY A  80 "
       model="   2" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.520 -0.069 1.60e-02 3.91e+03 1.85e+01
  bond model="   2" pdb=" N   TYR A  89 "
       model="   2" pdb=" CA  TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.527 -0.069 1.90e-02 2.77e+03 1.33e+01
  bond model="   2" pdb=" C   THR A  92 "
       model="   2" pdb=" N   LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.282  0.047 1.40e-02 5.10e+03 1.13e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       85.45 -    96.39: 3
       96.39 -   107.33: 498
      107.33 -   118.28: 2606
      118.28 -   129.22: 966
      129.22 -   140.16: 6
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" C   LYS A  79 "
        model="   2" pdb=" N   GLY A  80 "
        model="   2" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  140.16  -18.46 1.80e+00 3.09e-01 1.05e+02
  angle model="   2" pdb=" C   HIS A 138 "
        model="   2" pdb=" N   HIS A 139 "
        model="   2" pdb=" CA  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     121.70  136.37  -14.67 1.80e+00 3.09e-01 6.64e+01
  angle model="   2" pdb=" C   SER A  97 "
        model="   2" pdb=" CA  SER A  97 "
        model="   2" pdb=" HA  SER A  97 "
      ideal   model   delta    sigma   weight residual
     109.00   85.45   23.55 3.00e+00 1.11e-01 6.16e+01
  angle model="   2" pdb=" C   SER A  90 "
        model="   2" pdb=" N   TYR A  91 "
        model="   2" pdb=" CA  TYR A  91 "
      ideal   model   delta    sigma   weight residual
     121.70  134.61  -12.91 1.80e+00 3.09e-01 5.14e+01
  angle model="   2" pdb=" OG1 THR A  92 "
        model="   2" pdb=" CB  THR A  92 "
        model="   2" pdb=" CG2 THR A  92 "
      ideal   model   delta    sigma   weight residual
     109.30  123.17  -13.87 2.00e+00 2.50e-01 4.81e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.39: 969
       26.39 -    52.78: 44
       52.78 -    79.16: 9
       79.16 -   105.55: 2
      105.55 -   131.94: 1
  Dihedral angle restraints: 1025
    sinusoidal: 562
      harmonic: 463
  Sorted by residual:
  dihedral model="   2" pdb=" CA  LYS A  79 "
           model="   2" pdb=" C   LYS A  79 "
           model="   2" pdb=" N   GLY A  80 "
           model="   2" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -48.06 -131.94     0      5.00e+00 4.00e-02 6.96e+02
  dihedral model="   2" pdb=" CA  TYR A  89 "
           model="   2" pdb=" C   TYR A  89 "
           model="   2" pdb=" N   SER A  90 "
           model="   2" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -81.54  -98.46     0      5.00e+00 4.00e-02 3.88e+02
  dihedral model="   2" pdb=" CA  THR A  92 "
           model="   2" pdb=" C   THR A  92 "
           model="   2" pdb=" N   LEU A  93 "
           model="   2" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   83.94   96.06     0      5.00e+00 4.00e-02 3.69e+02
  ... (remaining 1022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.064: 170
       1.064 -    2.128: 1
       2.128 -    3.191: 0
       3.191 -    4.255: 0
       4.255 -    5.319: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CB  ILE A  78 "
            model="   2" pdb=" CA  ILE A  78 "
            model="   2" pdb=" CG1 ILE A  78 "
            model="   2" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.67    5.32 2.00e-01 2.50e+01 7.07e+02
  chirality model="   2" pdb=" CA  LYS A  79 "
            model="   2" pdb=" N   LYS A  79 "
            model="   2" pdb=" C   LYS A  79 "
            model="   2" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.75    5.26 2.00e-01 2.50e+01 6.93e+02
  chirality model="   2" pdb=" CA  ILE A  78 "
            model="   2" pdb=" N   ILE A  78 "
            model="   2" pdb=" C   ILE A  78 "
            model="   2" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -2.35    4.78 2.00e-01 2.50e+01 5.72e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  12 "    0.090 2.00e-02 2.50e+03   4.75e-02 6.78e+01
        model="   2" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  12 "   -0.027 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  12 "    0.100 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  12 "   -0.055 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  12 "   -0.066 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  50 "   -0.115 2.00e-02 2.50e+03   4.49e-02 6.04e+01
        model="   2" pdb=" CG  TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  50 "    0.026 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  50 "   -0.068 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  50 "    0.041 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  50 "    0.045 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  PHE A  45 "   -0.031 2.00e-02 2.50e+03   4.30e-02 5.55e+01
        model="   2" pdb=" CG  PHE A  45 "   -0.023 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 PHE A  45 "    0.026 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 PHE A  45 "   -0.015 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 PHE A  45 "   -0.015 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 PHE A  45 "    0.026 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  PHE A  45 "   -0.013 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 PHE A  45 "    0.087 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 PHE A  45 "   -0.037 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 PHE A  45 "   -0.044 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 PHE A  45 "    0.079 2.00e-02 2.50e+03
        model="   2" pdb=" HZ  PHE A  45 "   -0.038 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 145
        2.16 -     2.77: 4131
        2.77 -     3.38: 6458
        3.38 -     3.99: 7865
        3.99 -     4.60: 11762
  Nonbonded interactions: 30361
  Sorted by model distance:
  nonbonded model="   2" pdb=" HA  ILE A  77 "
            model="   2" pdb=" H   LYS A  79 "
     model   vdw
     1.553 2.270
  nonbonded model="   2" pdb=" HD3 LYS A  79 "
            model="   2" pdb=" H   TYR A  81 "
     model   vdw
     1.633 2.270
  nonbonded model="   2" pdb=" HB  THR A  92 "
            model="   2" pdb=" HB2 LEU A  93 "
     model   vdw
     1.718 2.440
  nonbonded model="   2" pdb=" HA  SER A  76 "
            model="   2" pdb=" HB2 LYS A  79 "
     model   vdw
     1.738 2.440
  nonbonded model="   2" pdb=" HG  SER A  17 "
            model="   2" pdb=" OD1 ASP A  74 "
     model   vdw
     1.770 1.850
  ... (remaining 30356 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  ASP A  74 "
        model="   7" pdb=" CB  ILE A  78 "
        model="   7" pdb=" CB  LYS A  79 "
        model="   7" pdb=" CB  TYR A  89 "
        model="   7" pdb=" CB  SER A  90 "
        model="   7" pdb=" CB  LYS A 125 "
        model="   7" pdb=" CB  VAL A 126 "
        model="   7" pdb=" CB  MET A 128 "
        model="   7" pdb=" CB  SER A 130 "
  Number of C-beta restraints generated:  244

  Time building geometry restraints manager: 0.89 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.12
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CB  LYS A  79 "
        model="   4" pdb=" CB  TYR A  89 "
        model="   4" pdb=" CB  SER A  97 "
        model="   4" pdb=" CB  VAL A 126 "
        model="   4" pdb=" CB  ILE A 131 "
  Number of C-beta restraints generated:  250

  Time building geometry restraints manager: 3.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 57
        1.23 -     1.43: 423
        1.43 -     1.62: 649
        1.62 -     1.82: 7
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" CA  ALA A 124 "
       model="   7" pdb=" C   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.525  1.325  0.200 2.10e-02 2.27e+03 9.09e+01
  bond model="   7" pdb=" CA  GLY A 121 "
       model="   7" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.663 -0.147 1.80e-02 3.09e+03 6.71e+01
  bond model="   7" pdb=" N   GLY A  80 "
       model="   7" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.574 -0.123 1.60e-02 3.91e+03 5.88e+01
  bond model="   7" pdb=" N   ILE A 122 "
       model="   7" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.599 -0.141 1.90e-02 2.77e+03 5.50e+01
  bond model="   7" pdb=" CA  LYS A 125 "
       model="   7" pdb=" C   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.525  1.369  0.156 2.10e-02 2.27e+03 5.49e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       40.83 -    62.75: 1
       62.75 -    84.67: 1
       84.67 -   106.60: 248
      106.60 -   128.52: 3800
      128.52 -   150.44: 29
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" N   ILE A  78 "
        model="   7" pdb=" CA  ILE A  78 "
        model="   7" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.00   40.83   69.17 3.00e+00 1.11e-01 5.32e+02
  angle model="   7" pdb=" C   VAL A 126 "
        model="   7" pdb=" CA  VAL A 126 "
        model="   7" pdb=" CB  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     111.40  150.14  -38.74 1.90e+00 2.77e-01 4.16e+02
  angle model="   7" pdb=" N   VAL A 126 "
        model="   7" pdb=" CA  VAL A 126 "
        model="   7" pdb=" HA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     110.00  150.44  -40.44 3.00e+00 1.11e-01 1.82e+02
  angle model="   7" pdb=" CB  LYS A  79 "
        model="   7" pdb=" CG  LYS A  79 "
        model="   7" pdb=" CD  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     111.30  139.46  -28.16 2.30e+00 1.89e-01 1.50e+02
  angle model="   7" pdb=" C   LYS A 125 "
        model="   7" pdb=" N   VAL A 126 "
        model="   7" pdb=" CA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     121.70  100.35   21.35 1.80e+00 3.09e-01 1.41e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.96: 947
       26.96 -    53.93: 49
       53.93 -    80.89: 10
       80.89 -   107.85: 6
      107.85 -   134.82: 1
  Dihedral angle restraints: 1013
    sinusoidal: 562
      harmonic: 451
  Sorted by residual:
  dihedral model="   7" pdb=" CA  TYR A  89 "
           model="   7" pdb=" C   TYR A  89 "
           model="   7" pdb=" N   SER A  90 "
           model="   7" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -45.18 -134.82     0      5.00e+00 4.00e-02 7.27e+02
  dihedral model="   7" pdb=" CA  ILE A 122 "
           model="   7" pdb=" C   ILE A 122 "
           model="   7" pdb=" N   GLU A 123 "
           model="   7" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -73.20 -106.80     0      5.00e+00 4.00e-02 4.56e+02
  dihedral model="   7" pdb=" CA  ILE A  78 "
           model="   7" pdb=" C   ILE A  78 "
           model="   7" pdb=" N   LYS A  79 "
           model="   7" pdb=" CA  LYS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -73.58 -106.42     0      5.00e+00 4.00e-02 4.53e+02
  ... (remaining 1010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.247: 164
       1.247 -    2.494: 0
       2.494 -    3.741: 3
       3.741 -    4.988: 7
       4.988 -    6.234: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CA  LYS A  79 "
            model="   7" pdb=" N   LYS A  79 "
            model="   7" pdb=" C   LYS A  79 "
            model="   7" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.72    6.23 2.00e-01 2.50e+01 9.72e+02
  chirality model="   7" pdb=" CB  ILE A 131 "
            model="   7" pdb=" CA  ILE A 131 "
            model="   7" pdb=" CG1 ILE A 131 "
            model="   7" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.64    5.29 2.00e-01 2.50e+01 6.99e+02
  chirality model="   7" pdb=" CB  THR A  92 "
            model="   7" pdb=" CA  THR A  92 "
            model="   7" pdb=" OG1 THR A  92 "
            model="   7" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.35    4.91 2.00e-01 2.50e+01 6.02e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  PHE A  67 "   -0.140 2.00e-02 2.50e+03   5.79e-02 1.00e+02
        model="   7" pdb=" CG  PHE A  67 "    0.022 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 PHE A  67 "    0.035 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 PHE A  67 "    0.032 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 PHE A  67 "    0.009 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 PHE A  67 "    0.011 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  PHE A  67 "   -0.035 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 PHE A  67 "    0.060 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 PHE A  67 "    0.053 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 PHE A  67 "    0.021 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 PHE A  67 "    0.027 2.00e-02 2.50e+03
        model="   7" pdb=" HZ  PHE A  67 "   -0.094 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  81 "    0.138 2.00e-02 2.50e+03   5.68e-02 9.69e+01
        model="   7" pdb=" CG  TYR A  81 "   -0.011 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  81 "   -0.034 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  81 "   -0.027 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  81 "   -0.011 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  81 "   -0.017 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  81 "    0.016 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  81 "    0.099 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  81 "   -0.063 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  81 "   -0.044 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  81 "   -0.032 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CA  ILE A  78 "    0.043 2.00e-02 2.50e+03   8.48e-02 7.19e+01
        model="   7" pdb=" C   ILE A  78 "   -0.147 2.00e-02 2.50e+03
        model="   7" pdb=" O   ILE A  78 "    0.054 2.00e-02 2.50e+03
        model="   7" pdb=" N   LYS A  79 "    0.050 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.34 -     1.99: 57
        1.99 -     2.64: 2936
        2.64 -     3.30: 6970
        3.30 -     3.95: 8419
        3.95 -     4.60: 12702
  Nonbonded interactions: 31084
  Sorted by model distance:
  nonbonded model="   7" pdb=" H   ILE A 131 "
            model="   7" pdb=" H   LEU A 132 "
     model   vdw
     1.342 2.100
  nonbonded model="   7" pdb=" HG2 LYS A  79 "
            model="   7" pdb=" HA2 GLY A  80 "
     model   vdw
     1.514 2.440
  nonbonded model="   7" pdb=" HE3 LYS A  79 "
            model="   7" pdb=" H   ASP A  95 "
     model   vdw
     1.562 2.270
  nonbonded model="   7" pdb=" HA  LYS A 125 "
            model="   7" pdb=" H   ARG A 127 "
     model   vdw
     1.592 2.270
  nonbonded model="   7" pdb=" HB  ILE A  78 "
            model="   7" pdb=" HB2 LYS A  79 "
     model   vdw
     1.642 2.440
  ... (remaining 31079 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 40
        1.23 -     1.42: 437
        1.42 -     1.62: 645
        1.62 -     1.81: 14
  Bond restraints: 2242
  Sorted by residual:
  bond model="   4" pdb=" N   VAL A 126 "
       model="   4" pdb=" CA  VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.718 -0.260 1.90e-02 2.77e+03 1.87e+02
  bond model="   4" pdb=" N   LEU A 119 "
       model="   4" pdb=" CA  LEU A 119 "
    ideal  model  delta    sigma   weight residual
    1.458  1.671 -0.213 1.90e-02 2.77e+03 1.25e+02
  bond model="   4" pdb=" CA  GLY A 121 "
       model="   4" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.706 -0.190 1.80e-02 3.09e+03 1.12e+02
  bond model="   4" pdb=" N   ILE A 122 "
       model="   4" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.653 -0.195 1.90e-02 2.77e+03 1.05e+02
  bond model="   4" pdb=" N   LYS A  79 "
       model="   4" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.640 -0.182 1.90e-02 2.77e+03 9.22e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       14.51 -    39.82: 1
       39.82 -    65.13: 0
       65.13 -    90.44: 7
       90.44 -   115.75: 2960
      115.75 -   141.07: 1111
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   4" pdb=" C   ILE A 131 "
        model="   4" pdb=" CA  ILE A 131 "
        model="   4" pdb=" HA  ILE A 131 "
      ideal   model   delta    sigma   weight residual
     109.00   14.51   94.49 3.00e+00 1.11e-01 9.92e+02
  angle model="   4" pdb=" N   ILE A 122 "
        model="   4" pdb=" CA  ILE A 122 "
        model="   4" pdb=" CB  ILE A 122 "
      ideal   model   delta    sigma   weight residual
     111.50   88.54   22.96 1.70e+00 3.46e-01 1.82e+02
  angle model="   4" pdb=" CA  LYS A 125 "
        model="   4" pdb=" C   LYS A 125 "
        model="   4" pdb=" N   VAL A 126 "
      ideal   model   delta    sigma   weight residual
     116.20   89.90   26.30 2.00e+00 2.50e-01 1.73e+02
  angle model="   4" pdb=" C   ILE A  78 "
        model="   4" pdb=" CA  ILE A  78 "
        model="   4" pdb=" CB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     111.60  137.22  -25.62 2.00e+00 2.50e-01 1.64e+02
  angle model="   4" pdb=" C   ASP A 118 "
        model="   4" pdb=" N   LEU A 119 "
        model="   4" pdb=" CA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     121.70  141.07  -19.37 1.80e+00 3.09e-01 1.16e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.58: 938
       22.58 -    45.16: 57
       45.16 -    67.74: 17
       67.74 -    90.33: 5
       90.33 -   112.91: 2
  Dihedral angle restraints: 1019
    sinusoidal: 562
      harmonic: 457
  Sorted by residual:
  dihedral model="   4" pdb=" CA  VAL A 126 "
           model="   4" pdb=" C   VAL A 126 "
           model="   4" pdb=" N   ARG A 127 "
           model="   4" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -67.09 -112.91     0      5.00e+00 4.00e-02 5.10e+02
  dihedral model="   4" pdb=" CA  LYS A 125 "
           model="   4" pdb=" C   LYS A 125 "
           model="   4" pdb=" N   VAL A 126 "
           model="   4" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   70.72  109.28     0      5.00e+00 4.00e-02 4.78e+02
  dihedral model="   4" pdb=" CA  LEU A 119 "
           model="   4" pdb=" C   LEU A 119 "
           model="   4" pdb=" N   GLU A 120 "
           model="   4" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   94.09   85.91     0      5.00e+00 4.00e-02 2.95e+02
  ... (remaining 1016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.224: 167
       1.224 -    2.449: 1
       2.449 -    3.673: 2
       3.673 -    4.897: 2
       4.897 -    6.122: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CA  LYS A  79 "
            model="   4" pdb=" N   LYS A  79 "
            model="   4" pdb=" C   LYS A  79 "
            model="   4" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.61    6.12 2.00e-01 2.50e+01 9.37e+02
  chirality model="   4" pdb=" CA  VAL A 126 "
            model="   4" pdb=" N   VAL A 126 "
            model="   4" pdb=" C   VAL A 126 "
            model="   4" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44   -3.63    6.07 2.00e-01 2.50e+01 9.21e+02
  chirality model="   4" pdb=" CB  ILE A  78 "
            model="   4" pdb=" CA  ILE A  78 "
            model="   4" pdb=" CG1 ILE A  78 "
            model="   4" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.81    5.46 2.00e-01 2.50e+01 7.44e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CA  LYS A 125 "    0.071 2.00e-02 2.50e+03   1.52e-01 2.31e+02
        model="   4" pdb=" C   LYS A 125 "   -0.262 2.00e-02 2.50e+03
        model="   4" pdb=" O   LYS A 125 "    0.115 2.00e-02 2.50e+03
        model="   4" pdb=" N   VAL A 126 "    0.076 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  91 "    0.168 2.00e-02 2.50e+03   7.75e-02 1.80e+02
        model="   4" pdb=" CG  TYR A  91 "    0.026 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  91 "   -0.054 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  91 "   -0.021 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  91 "    0.011 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  91 "   -0.024 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  91 "    0.031 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  91 "    0.085 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  91 "   -0.151 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  91 "   -0.051 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  91 "    0.042 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  91 "   -0.062 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  89 "   -0.152 2.00e-02 2.50e+03   6.44e-02 1.24e+02
        model="   4" pdb=" CG  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  89 "    0.027 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  89 "    0.038 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  89 "    0.020 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  89 "    0.009 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  89 "   -0.026 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  89 "   -0.108 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  89 "    0.050 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  89 "    0.083 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  89 "    0.046 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  89 "    0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 136
        2.14 -     2.75: 3855
        2.75 -     3.37: 6417
        3.37 -     3.98: 7777
        3.98 -     4.60: 11550
  Nonbonded interactions: 29735
  Sorted by model distance:
  nonbonded model="   4" pdb=" O   ILE A 131 "
            model="   4" pdb=" HA  ILE A 131 "
     model   vdw
     1.520 2.096
  nonbonded model="   4" pdb=" HA  MET A 128 "
            model="   4" pdb=" H   SER A 130 "
     model   vdw
     1.569 2.270
  nonbonded model="   4" pdb=" H   GLY A  80 "
            model="   4" pdb=" H   ASP A  95 "
     model   vdw
     1.586 2.100
  nonbonded model="   4" pdb="HG22 ILE A  71 "
            model="   4" pdb="HD21 LEU A  99 "
     model   vdw
     1.628 2.440
  nonbonded model="   4" pdb=" HA2 GLY A  94 "
            model="   4" pdb=" H   GLY A  96 "
     model   vdw
     1.677 2.270
  ... (remaining 29730 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 94
        1.23 -     1.43: 378
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  10" pdb=" CZ  ARG A 129 "
       model="  10" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.05e+00
  bond model="  10" pdb=" CD2 HIS A 139 "
       model="  10" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.56e+00
  bond model="  10" pdb=" CD2 HIS A 136 "
       model="  10" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.77e+00
  bond model="  10" pdb=" CZ  ARG A 127 "
       model="  10" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.68e+00
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.62e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       95.38 -   103.14: 14
      103.14 -   110.90: 2323
      110.90 -   118.66: 823
      118.66 -   126.42: 895
      126.42 -   134.18: 24
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  10" pdb=" C   LEU A  93 "
        model="  10" pdb=" N   GLY A  94 "
        model="  10" pdb=" CA  GLY A  94 "
      ideal   model   delta    sigma   weight residual
     121.70  134.18  -12.48 1.80e+00 3.09e-01 4.81e+01
  angle model="  10" pdb=" C   LEU A  93 "
        model="  10" pdb=" CA  LEU A  93 "
        model="  10" pdb=" CB  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.10  120.61  -10.51 1.90e+00 2.77e-01 3.06e+01
  angle model="  10" pdb=" OE1 GLN A  66 "
        model="  10" pdb=" CD  GLN A  66 "
        model="  10" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.63    4.97 1.00e+00 1.00e+00 2.47e+01
  angle model="  10" pdb=" C   LEU A  93 "
        model="  10" pdb=" CA  LEU A  93 "
        model="  10" pdb=" HA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     109.00   95.38   13.62 3.00e+00 1.11e-01 2.06e+01
  angle model="  10" pdb=" CA  THR A  92 "
        model="  10" pdb=" CB  THR A  92 "
        model="  10" pdb=" CG2 THR A  92 "
      ideal   model   delta    sigma   weight residual
     110.50  117.72   -7.22 1.70e+00 3.46e-01 1.80e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.68: 889
       12.68 -    25.37: 89
       25.37 -    38.05: 28
       38.05 -    50.74: 18
       50.74 -    63.42: 9
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  10" pdb=" CA  TYR A  91 "
           model="  10" pdb=" C   TYR A  91 "
           model="  10" pdb=" N   THR A  92 "
           model="  10" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.06  -47.94     0      5.00e+00 4.00e-02 9.19e+01
  dihedral model="  10" pdb=" CA  LEU A  93 "
           model="  10" pdb=" C   LEU A  93 "
           model="  10" pdb=" N   GLY A  94 "
           model="  10" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.78  -41.22     0      5.00e+00 4.00e-02 6.80e+01
  dihedral model="  10" pdb=" CA  THR A  92 "
           model="  10" pdb=" C   THR A  92 "
           model="  10" pdb=" N   LEU A  93 "
           model="  10" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.63  -37.37     0      5.00e+00 4.00e-02 5.59e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 135
       0.107 -    0.213: 36
       0.213 -    0.320: 2
       0.320 -    0.426: 1
       0.426 -    0.533: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CA  LEU A  93 "
            model="  10" pdb=" N   LEU A  93 "
            model="  10" pdb=" C   LEU A  93 "
            model="  10" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.10e+00
  chirality model="  10" pdb=" CG  LEU A  93 "
            model="  10" pdb=" CB  LEU A  93 "
            model="  10" pdb=" CD1 LEU A  93 "
            model="  10" pdb=" CD2 LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.11   -0.48 2.00e-01 2.50e+01 5.66e+00
  chirality model="  10" pdb=" CA  TYR A  91 "
            model="  10" pdb=" N   TYR A  91 "
            model="  10" pdb=" C   TYR A  91 "
            model="  10" pdb=" CB  TYR A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.28e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  50 "    0.175 2.00e-02 2.50e+03   8.34e-02 2.09e+02
        model="  10" pdb=" CG  TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  50 "   -0.029 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  50 "   -0.039 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  50 "   -0.039 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  50 "   -0.029 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  50 "    0.186 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  50 "   -0.035 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  50 "   -0.066 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  50 "   -0.076 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  50 "   -0.045 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  81 "    0.160 2.00e-02 2.50e+03   7.02e-02 1.48e+02
        model="  10" pdb=" CG  TYR A  81 "   -0.008 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  81 "   -0.033 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  81 "   -0.032 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  81 "   -0.026 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  81 "    0.147 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  81 "   -0.055 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  81 "   -0.051 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  81 "   -0.037 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  81 "   -0.038 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  91 "   -0.122 2.00e-02 2.50e+03   6.55e-02 1.29e+02
        model="  10" pdb=" CG  TYR A  91 "   -0.024 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  91 "    0.008 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  91 "    0.035 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  91 "    0.036 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  91 "   -0.131 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  91 "    0.011 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  91 "    0.093 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  91 "    0.086 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  91 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 118
        2.16 -     2.77: 4035
        2.77 -     3.38: 6271
        3.38 -     3.99: 7615
        3.99 -     4.60: 11321
  Nonbonded interactions: 29360
  Sorted by model distance:
  nonbonded model="  10" pdb="HD11 LEU A  64 "
            model="  10" pdb="HD22 LEU A  93 "
     model   vdw
     1.547 2.440
  nonbonded model="  10" pdb="HD13 LEU A  64 "
            model="  10" pdb="HG11 VAL A 104 "
     model   vdw
     1.617 2.440
  nonbonded model="  10" pdb="HG22 THR A  92 "
            model="  10" pdb=" H   LEU A  93 "
     model   vdw
     1.658 2.270
  nonbonded model="  10" pdb=" OD1 ASP A  74 "
            model="  10" pdb=" HG  SER A  76 "
     model   vdw
     1.802 1.850
  nonbonded model="  10" pdb=" OE2 GLU A  24 "
            model="  10" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.803 1.850
  ... (remaining 29355 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  12" pdb=" CB  GLU A 120 "
        model="  12" pdb=" CB  ARG A 127 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 1.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 71
        1.23 -     1.42: 401
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" CZ  ARG A  58 "
       model="  12" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.79e+00
  bond model="  12" pdb=" CZ  ARG A  21 "
       model="  12" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.54e+00
  bond model="  12" pdb=" CZ  ARG A 129 "
       model="  12" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.28e+00
  bond model="  12" pdb=" CD2 HIS A 139 "
       model="  12" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.09e+00
  bond model="  12" pdb=" ND1 HIS A 136 "
       model="  12" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.20e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       96.28 -   103.61: 27
      103.61 -   110.95: 2294
      110.95 -   118.29: 804
      118.29 -   125.62: 907
      125.62 -   132.96: 47
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" C   LEU A 119 "
        model="  12" pdb=" N   GLU A 120 "
        model="  12" pdb=" CA  GLU A 120 "
      ideal   model   delta    sigma   weight residual
     121.70  132.96  -11.26 1.80e+00 3.09e-01 3.91e+01
  angle model="  12" pdb=" C   VAL A 126 "
        model="  12" pdb=" N   ARG A 127 "
        model="  12" pdb=" CA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     121.70  132.01  -10.31 1.80e+00 3.09e-01 3.28e+01
  angle model="  12" pdb=" N   ARG A 127 "
        model="  12" pdb=" CA  ARG A 127 "
        model="  12" pdb=" HA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     110.00   96.28   13.72 3.00e+00 1.11e-01 2.09e+01
  angle model="  12" pdb=" OE1 GLN A 100 "
        model="  12" pdb=" CD  GLN A 100 "
        model="  12" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.36    4.24 1.00e+00 1.00e+00 1.80e+01
  angle model="  12" pdb=" CB  HIS A 136 "
        model="  12" pdb=" CG  HIS A 136 "
        model="  12" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  125.76    5.44 1.30e+00 5.92e-01 1.75e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 928
       17.54 -    35.07: 69
       35.07 -    52.61: 21
       52.61 -    70.14: 5
       70.14 -    87.68: 6
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  12" pdb=" CA  ILE A  51 "
           model="  12" pdb=" C   ILE A  51 "
           model="  12" pdb=" N   PRO A  52 "
           model="  12" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.98   27.02     0      5.00e+00 4.00e-02 2.92e+01
  dihedral model="  12" pdb=" CA  ARG A 127 "
           model="  12" pdb=" C   ARG A 127 "
           model="  12" pdb=" N   MET A 128 "
           model="  12" pdb=" CA  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.05  -25.95     0      5.00e+00 4.00e-02 2.69e+01
  dihedral model="  12" pdb=" CA  GLY A 121 "
           model="  12" pdb=" C   GLY A 121 "
           model="  12" pdb=" N   ILE A 122 "
           model="  12" pdb=" CA  ILE A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.65  -24.35     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.926: 174
       0.926 -    1.852: 0
       1.852 -    2.778: 0
       2.778 -    3.705: 0
       3.705 -    4.631: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  GLU A 120 "
            model="  12" pdb=" N   GLU A 120 "
            model="  12" pdb=" C   GLU A 120 "
            model="  12" pdb=" CB  GLU A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.12    4.63 2.00e-01 2.50e+01 5.36e+02
  chirality model="  12" pdb=" CA  ARG A 127 "
            model="  12" pdb=" N   ARG A 127 "
            model="  12" pdb=" C   ARG A 127 "
            model="  12" pdb=" CB  ARG A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.47    3.98 2.00e-01 2.50e+01 3.96e+02
  chirality model="  12" pdb=" CB  ILE A 131 "
            model="  12" pdb=" CA  ILE A 131 "
            model="  12" pdb=" CG1 ILE A 131 "
            model="  12" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.55e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  81 "    0.096 2.00e-02 2.50e+03   1.42e-01 6.02e+02
        model="  12" pdb=" CG  TYR A  81 "    0.084 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  81 "   -0.087 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  81 "    0.053 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  81 "    0.070 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  81 "   -0.069 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  81 "    0.046 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  81 "    0.048 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  81 "   -0.314 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  81 "    0.113 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  81 "    0.188 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  81 "   -0.229 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  50 "    0.113 2.00e-02 2.50e+03   4.58e-02 6.28e+01
        model="  12" pdb=" CG  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  50 "   -0.029 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  50 "    0.055 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  50 "   -0.047 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  50 "   -0.069 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  50 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A 111 "    0.080 2.00e-02 2.50e+03   3.64e-02 3.97e+01
        model="  12" pdb=" CG  TYR A 111 "   -0.035 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A 111 "   -0.029 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A 111 "    0.054 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A 111 "   -0.045 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A 111 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.26: 260
        2.26 -     2.84: 4835
        2.84 -     3.43: 5654
        3.43 -     4.01: 7270
        4.01 -     4.60: 10870
  Nonbonded interactions: 28889
  Sorted by model distance:
  nonbonded model="  12" pdb=" H   ALA A 124 "
            model="  12" pdb="HH21 ARG A 127 "
     model   vdw
     1.670 2.100
  nonbonded model="  12" pdb="HG21 ILE A 122 "
            model="  12" pdb=" H   VAL A 126 "
     model   vdw
     1.773 2.270
  nonbonded model="  12" pdb="HG23 ILE A 122 "
            model="  12" pdb=" HB2 LYS A 125 "
     model   vdw
     1.789 2.440
  nonbonded model="  12" pdb=" HZ1 LYS A  10 "
            model="  12" pdb=" OD1 ASP A  23 "
     model   vdw
     1.823 1.850
  nonbonded model="  12" pdb=" HB3 SER A  46 "
            model="  12" pdb=" H   HIS A 134 "
     model   vdw
     1.825 2.270
  ... (remaining 28884 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.69
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CB  LYS A  79 "
        model="   3" pdb=" CB  TYR A  89 "
        model="   3" pdb=" CB  SER A  97 "
        model="   3" pdb=" CB  ILE A 122 "
        model="   3" pdb=" CB  GLU A 123 "
        model="   3" pdb=" CB  VAL A 126 "
        model="   3" pdb=" CB  ARG A 127 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 0.77 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.12 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 70
        1.23 -     1.43: 408
        1.43 -     1.62: 654
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   3" pdb=" N   LYS A  79 "
       model="   3" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.563 -0.105 1.90e-02 2.77e+03 3.06e+01
  bond model="   3" pdb=" N   GLY A  80 "
       model="   3" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.536 -0.085 1.60e-02 3.91e+03 2.85e+01
  bond model="   3" pdb=" N   SER A 130 "
       model="   3" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.551 -0.093 1.90e-02 2.77e+03 2.42e+01
  bond model="   3" pdb=" N   ARG A 127 "
       model="   3" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.368  0.090 1.90e-02 2.77e+03 2.23e+01
  bond model="   3" pdb=" CA  LYS A  79 "
       model="   3" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.618 -0.093 2.10e-02 2.27e+03 1.97e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       68.23 -    84.64: 2
       84.64 -   101.04: 29
      101.04 -   117.44: 3031
      117.44 -   133.85: 1010
      133.85 -   150.25: 7
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   3" pdb=" C   ILE A  78 "
        model="   3" pdb=" CA  ILE A  78 "
        model="   3" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   68.23   40.77 3.00e+00 1.11e-01 1.85e+02
  angle model="   3" pdb=" N   ILE A  78 "
        model="   3" pdb=" CA  ILE A  78 "
        model="   3" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.00  150.25  -40.25 3.00e+00 1.11e-01 1.80e+02
  angle model="   3" pdb=" C   ILE A  78 "
        model="   3" pdb=" CA  ILE A  78 "
        model="   3" pdb=" CB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     111.60  135.47  -23.87 2.00e+00 2.50e-01 1.42e+02
  angle model="   3" pdb=" CB  ILE A  78 "
        model="   3" pdb=" CA  ILE A  78 "
        model="   3" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   78.35   30.65 3.00e+00 1.11e-01 1.04e+02
  angle model="   3" pdb=" C   TYR A  91 "
        model="   3" pdb=" N   THR A  92 "
        model="   3" pdb=" CA  THR A  92 "
      ideal   model   delta    sigma   weight residual
     121.70  140.06  -18.36 1.80e+00 3.09e-01 1.04e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 898
       17.26 -    34.51: 72
       34.51 -    51.77: 30
       51.77 -    69.02: 9
       69.02 -    86.28: 8
  Dihedral angle restraints: 1017
    sinusoidal: 562
      harmonic: 455
  Sorted by residual:
  dihedral model="   3" pdb=" C   ILE A  78 "
           model="   3" pdb=" N   ILE A  78 "
           model="   3" pdb=" CA  ILE A  78 "
           model="   3" pdb=" CB  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -171.03   49.03     0      2.50e+00 1.60e-01 3.85e+02
  dihedral model="   3" pdb=" N   ILE A  78 "
           model="   3" pdb=" C   ILE A  78 "
           model="   3" pdb=" CA  ILE A  78 "
           model="   3" pdb=" CB  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  167.96  -44.56     0      2.50e+00 1.60e-01 3.18e+02
  dihedral model="   3" pdb=" CA  SER A 130 "
           model="   3" pdb=" C   SER A 130 "
           model="   3" pdb=" N   ILE A 131 "
           model="   3" pdb=" CA  ILE A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -93.72  -86.28     0      5.00e+00 4.00e-02 2.98e+02
  ... (remaining 1014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.089: 164
       1.089 -    2.178: 1
       2.178 -    3.267: 0
       3.267 -    4.356: 1
       4.356 -    5.445: 10
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   3" pdb=" CA  LYS A  79 "
            model="   3" pdb=" N   LYS A  79 "
            model="   3" pdb=" C   LYS A  79 "
            model="   3" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.93    5.45 2.00e-01 2.50e+01 7.41e+02
  chirality model="   3" pdb=" CB  ILE A 131 "
            model="   3" pdb=" CA  ILE A 131 "
            model="   3" pdb=" CG1 ILE A 131 "
            model="   3" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.53    5.18 2.00e-01 2.50e+01 6.71e+02
  chirality model="   3" pdb=" CA  VAL A 126 "
            model="   3" pdb=" N   VAL A 126 "
            model="   3" pdb=" C   VAL A 126 "
            model="   3" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44   -2.65    5.09 2.00e-01 2.50e+01 6.48e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  91 "   -0.144 2.00e-02 2.50e+03   6.51e-02 1.27e+02
        model="   3" pdb=" CG  TYR A  91 "    0.017 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  91 "    0.046 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  91 "    0.017 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  91 "    0.033 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  91 "   -0.110 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  91 "    0.096 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  91 "   -0.029 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  91 "    0.066 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  12 "   -0.120 2.00e-02 2.50e+03   5.15e-02 7.95e+01
        model="   3" pdb=" CG  TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  12 "   -0.101 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  12 "    0.051 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  12 "    0.030 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  12 "    0.018 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  12 "    0.037 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  89 "   -0.091 2.00e-02 2.50e+03   4.33e-02 5.63e+01
        model="   3" pdb=" CG  TYR A  89 "    0.029 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  89 "    0.037 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  89 "   -0.011 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  89 "    0.019 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  89 "   -0.042 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  89 "    0.074 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  89 "   -0.012 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  89 "   -0.050 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  89 "    0.037 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.10: 96
        2.10 -     2.72: 3672
        2.72 -     3.35: 6693
        3.35 -     3.97: 8408
        3.97 -     4.60: 12607
  Nonbonded interactions: 31476
  Sorted by model distance:
  nonbonded model="   3" pdb=" HA  ILE A  78 "
            model="   3" pdb=" HB  ILE A  78 "
     model   vdw
     1.469 1.952
  nonbonded model="   3" pdb=" H   ASP A  95 "
            model="   3" pdb=" H   GLY A  96 "
     model   vdw
     1.622 2.100
  nonbonded model="   3" pdb=" HB2 TYR A  91 "
            model="   3" pdb=" H   THR A  92 "
     model   vdw
     1.689 2.270
  nonbonded model="   3" pdb=" H   THR A  92 "
            model="   3" pdb=" HA  THR A  92 "
     model   vdw
     1.704 1.816
  nonbonded model="   3" pdb=" O   ILE A  77 "
            model="   3" pdb=" H   SER A  97 "
     model   vdw
     1.787 1.850
  ... (remaining 31471 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 462
        1.42 -     1.61: 669
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   8" pdb=" N   MET A   1 "
       model="   8" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.44e+00
  bond model="   8" pdb=" CZ  ARG A 127 "
       model="   8" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.326  0.004 1.30e-02 5.92e+03 8.32e-02
  bond model="   8" pdb=" NE  ARG A  58 "
       model="   8" pdb=" CZ  ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 7.30e-02
  bond model="   8" pdb=" CZ  ARG A  58 "
       model="   8" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 6.86e-02
  bond model="   8" pdb=" NE  ARG A 127 "
       model="   8" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 6.52e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.90 -   106.90: 66
      106.90 -   112.89: 2719
      112.89 -   118.89: 426
      118.89 -   124.88: 824
      124.88 -   130.87: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   8" pdb=" CB  PRO A 102 "
        model="   8" pdb=" CA  PRO A 102 "
        model="   8" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.59e+00
  angle model="   8" pdb=" CB  PRO A  52 "
        model="   8" pdb=" CA  PRO A  52 "
        model="   8" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   8" pdb=" CB  PRO A  54 "
        model="   8" pdb=" CA  PRO A  54 "
        model="   8" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   8" pdb=" CB  PRO A   6 "
        model="   8" pdb=" CA  PRO A   6 "
        model="   8" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  angle model="   8" pdb=" CB  PRO A  22 "
        model="   8" pdb=" CA  PRO A  22 "
        model="   8" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 867
       16.86 -    33.71: 82
       33.71 -    50.57: 59
       50.57 -    67.43: 22
       67.43 -    84.29: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   8" pdb=" CB  GLU A  55 "
           model="   8" pdb=" CG  GLU A  55 "
           model="   8" pdb=" CD  GLU A  55 "
           model="   8" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.29  -84.29     1      3.00e+01 1.11e-03 9.60e+00
  dihedral model="   8" pdb=" CB  LYS A 113 "
           model="   8" pdb=" CG  LYS A 113 "
           model="   8" pdb=" CD  LYS A 113 "
           model="   8" pdb=" CE  LYS A 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.34   57.34     3      1.50e+01 4.44e-03 9.44e+00
  dihedral model="   8" pdb=" N   HIS A 134 "
           model="   8" pdb=" CA  HIS A 134 "
           model="   8" pdb=" CB  HIS A 134 "
           model="   8" pdb=" CG  HIS A 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.33   57.33     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 107
       0.019 -    0.038: 45
       0.038 -    0.057: 5
       0.057 -    0.075: 0
       0.075 -    0.094: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  ILE A 122 "
            model="   8" pdb=" N   ILE A 122 "
            model="   8" pdb=" C   ILE A 122 "
            model="   8" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.20e-01
  chirality model="   8" pdb=" CA  ILE A  51 "
            model="   8" pdb=" N   ILE A  51 "
            model="   8" pdb=" C   ILE A  51 "
            model="   8" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.15e-01
  chirality model="   8" pdb=" CA  ILE A  38 "
            model="   8" pdb=" N   ILE A  38 "
            model="   8" pdb=" C   ILE A  38 "
            model="   8" pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.15e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A 105 "   -0.000 2.00e-02 2.50e+03   1.31e-03 5.14e-02
        model="   8" pdb=" CG  TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A 105 "    0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A 105 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A 105 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  89 "   -0.000 2.00e-02 2.50e+03   1.10e-03 3.61e-02
        model="   8" pdb=" CG  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  PHE A  45 "   -0.001 2.00e-02 2.50e+03   1.08e-03 3.50e-02
        model="   8" pdb=" CG  PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 PHE A  45 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HZ  PHE A  45 "    0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 204
        2.18 -     2.78: 4569
        2.78 -     3.39: 5637
        3.39 -     3.99: 7129
        3.99 -     4.60: 10689
  Nonbonded interactions: 28228
  Sorted by model distance:
  nonbonded model="   8" pdb="HG12 VAL A  41 "
            model="   8" pdb="HG22 VAL A 112 "
     model   vdw
     1.572 2.440
  nonbonded model="   8" pdb="HD23 LEU A   9 "
            model="   8" pdb="HD22 LEU A  26 "
     model   vdw
     1.619 2.440
  nonbonded model="   8" pdb="HG23 ILE A  37 "
            model="   8" pdb="HD13 ILE A 108 "
     model   vdw
     1.699 2.440
  nonbonded model="   8" pdb="HG23 VAL A  41 "
            model="   8" pdb=" H   HIS A  43 "
     model   vdw
     1.743 2.270
  nonbonded model="   8" pdb="HG22 THR A  83 "
            model="   8" pdb="HD11 ILE A  86 "
     model   vdw
     1.746 2.440
  ... (remaining 28223 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.870)
  Mean delta:    0.013 (Z=  0.669)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG1       110.40   120.90   -10.50  1.70e+00  3.82e+01   6.2*sigma
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   131.84   -10.14  1.80e+00  3.17e+01   5.6*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   130.27    -8.57  1.80e+00  2.27e+01   4.8*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   130.02    -8.32  1.80e+00  2.14e+01   4.6*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   10.501 (Z=  6.177)
  Mean delta:    1.983 (Z=  1.096)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   151.94    28.06  5.00e+00  3.15e+01   5.6*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00  -152.28   -27.72  5.00e+00  3.07e+01   5.5*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   156.42    23.58  5.00e+00  2.22e+01   4.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   157.63    22.37  5.00e+00  2.00e+01   4.5*sigma

  Min. delta:    0.033
  Max. delta:   89.298
  Mean delta:   19.372

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  CA
   A  85  LYS  N
   A  85  LYS  C
   A  85  LYS  CB          2.51    -2.21     4.72  2.00e-01  5.56e+02  23.6*sigma
   A  84  GLU  CA
   A  84  GLU  N
   A  84  GLU  C
   A  84  GLU  CB          2.51    -1.97     4.48  2.00e-01  5.03e+02  22.4*sigma
   A  86  ILE  CA
   A  86  ILE  N
   A  86  ILE  C
   A  86  ILE  CB          2.43    -1.73     4.17  2.00e-01  4.34e+02  20.8*sigma

  Min. delta:    0.000
  Max. delta:    4.717
  Mean delta:    0.592

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.078       0.148      121.36   7.4*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.063       0.121       78.76   6.1*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.063       0.114       79.24   5.7*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  ND1
   A 138  HIS  CD2
   A 138  HIS  CE1
   A 138  HIS  NE2           0.070       0.097       73.26   4.8*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  ND1
   A 139  HIS  CD2
   A 139  HIS  CE1
   A 139  HIS  NE2           0.068       0.091       68.47   4.5*sigma
   A 133  GLU  CG
   A 133  GLU  CD
   A 133  GLU  OE1
   A 133  GLU  OE2           0.048       0.083       23.27   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.078
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  86  ILE  HA , Angle C-CA-HA, observed: 95.679, delta from target: 13.321

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.476
    Angle     :  1.819  13.321   4079  Z= 0.810
    Chirality :  0.592   4.717    176
    Planarity :  0.013   0.076    327
    Dihedral  : 15.841  89.298    769
    Min Nonbonded Distance : 1.804
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  : 10.95 %
      Favored  : 86.13 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  7.26 %
      Favored  : 86.29 %
    Cbeta Deviations :  2.27 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.78 (0.66), residues: 137
    helix: -0.47 (0.60), residues: 56
    sheet:  None (None), residues: 0
    loop : -1.76 (0.68), residues: 81
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.019   0.006   HIS A 137 
   PHE   0.063   0.016   PHE A  45 
   TYR   0.182   0.034   TYR A 111 
   ARG   0.020   0.005   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.019   0.006   HIS A 137 
   PHE   0.042   0.014   PHE A  45 
   TYR   0.148   0.036   TYR A 111 
   ARG   0.006   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  28  GLN

=================================== Summary ===================================

  Ramachandran outliers =   2.92 %
                favored =  86.13 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =     3
  Clashscore            =   1.35
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.82
  MolProbity score      =   2.12

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.907)
  Mean delta:    0.013 (Z=  0.673)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.19     5.41  1.00e+00  2.93e+01   5.4*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   130.49    -8.79  1.80e+00  2.39e+01   4.9*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   117.87     4.73  1.00e+00  2.23e+01   4.7*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  C         111.00   124.22   -13.22  2.80e+00  2.23e+01   4.7*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   116.70    -4.10  1.00e+00  1.68e+01   4.1*sigma
   A  37  ILE  CA
   A  37  ILE  CB
   A  37  ILE  CG2       110.50   117.45    -6.95  1.70e+00  1.67e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   13.217 (Z=  5.412)
  Mean delta:    2.040 (Z=  1.092)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -135.97   -44.03  5.00e+00  7.75e+01   8.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   138.08    41.92  5.00e+00  7.03e+01   8.4*sigma
   A 103  ASP  CA
   A 103  ASP  C
   A 104  VAL  N
   A 104  VAL  CA        180.00  -144.49   -35.51  5.00e+00  5.04e+01   7.1*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   146.33    33.67  5.00e+00  4.54e+01   6.7*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -151.27   -28.73  5.00e+00  3.30e+01   5.7*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   151.29    28.71  5.00e+00  3.30e+01   5.7*sigma
   A 106  ALA  CA
   A 106  ALA  C
   A 107  LEU  N
   A 107  LEU  CA        180.00  -152.64   -27.36  5.00e+00  3.00e+01   5.5*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   154.34    25.66  5.00e+00  2.63e+01   5.1*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   158.97    21.03  5.00e+00  1.77e+01   4.2*sigma
   A 105  TYR  CA
   A 105  TYR  C
   A 106  ALA  N
   A 106  ALA  CA        180.00  -159.37   -20.63  5.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.072
  Max. delta:   87.914
  Mean delta:   17.327

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -1.91     4.42  2.00e-01  4.88e+02  22.1*sigma

  Min. delta:    0.001
  Max. delta:    4.420
  Mean delta:    0.346

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.118       0.213      280.57  10.6*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.088       0.167      156.25   8.3*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.076       0.145      116.95   7.3*sigma
   A  45  PHE  CB
   A  45  PHE  CG
   A  45  PHE  CD1
   A  45  PHE  CD2
   A  45  PHE  CE1
   A  45  PHE  CE2
   A  45  PHE  CZ            0.072       0.112       91.41   5.6*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.053       0.102       55.26   5.1*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.092       0.092      167.54   4.6*sigma
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.050       0.091       49.68   4.5*sigma

  Min. delta:    0.000
  Max. delta:    0.118
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  93  LEU  HA , Angle C-CA-HA, observed: 94.071, delta from target: 14.929

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.479
    Angle     :  1.840  14.929   4079  Z= 0.807
    Chirality :  0.346   4.420    176
    Planarity :  0.015   0.110    327
    Dihedral  : 14.354  87.914    769
    Min Nonbonded Distance : 1.773
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  : 13.87 %
      Favored  : 83.94 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  : 11.29 %
      Favored  : 83.06 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 3.05 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.92 (0.70), residues: 137
    helix: -0.19 (0.64), residues: 56
    sheet:  None (None), residues: 0
    loop : -2.18 (0.71), residues: 81
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A 137 
   PHE   0.157   0.030   PHE A  45 
   TYR   0.257   0.044   TYR A  89 
   ARG   0.042   0.011   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A 137 
   PHE   0.112   0.032   PHE A  45 
   TYR   0.213   0.053   TYR A  89 
   ARG   0.013   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.768)
  Mean delta:    0.013 (Z=  0.653)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.44     5.16  1.00e+00  2.66e+01   5.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   117.98     4.62  1.00e+00  2.13e+01   4.6*sigma
   A 137  HIS  CA
   A 137  HIS  CB
   A 137  HIS  CG        113.80   118.24    -4.44  1.00e+00  1.97e+01   4.4*sigma
   A  29  ASP  CA
   A  29  ASP  CB
   A  29  ASP  CG        112.60   116.70    -4.10  1.00e+00  1.68e+01   4.1*sigma
   A 114  PRO  N
   A 114  PRO  CA
   A 114  PRO  CB        103.00   107.50    -4.50  1.10e+00  1.67e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.56     4.04  1.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.301 (Z=  5.158)
  Mean delta:    1.844 (Z=  1.033)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   134.04    45.96  5.00e+00  8.45e+01   9.2*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   150.80    29.20  5.00e+00  3.41e+01   5.8*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   153.83    26.17  5.00e+00  2.74e+01   5.2*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   153.94    26.06  5.00e+00  2.72e+01   5.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA          0.00    25.25   -25.25  5.00e+00  2.55e+01   5.0*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00  -155.98   -24.02  5.00e+00  2.31e+01   4.8*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   158.76    21.24  5.00e+00  1.80e+01   4.2*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -158.81   -21.19  5.00e+00  1.80e+01   4.2*sigma

  Min. delta:    0.004
  Max. delta:   88.210
  Mean delta:   17.367

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.459
  Mean delta:    0.098

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.109       0.213      236.64  10.7*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.074       0.105      110.85   5.3*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  ND1
   A 139  HIS  CD2
   A 139  HIS  CE1
   A 139  HIS  NE2           0.070       0.094       73.95   4.7*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  ND1
   A 137  HIS  CD2
   A 137  HIS  CE1
   A 137  HIS  NE2           0.063       0.093       59.02   4.6*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.098       0.085      193.81   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.109
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.465
    Angle     :  1.695   7.915   4079  Z= 0.761
    Chirality :  0.098   0.459    176
    Planarity :  0.015   0.114    327
    Dihedral  : 13.858  88.210    769
    Min Nonbonded Distance : 1.752
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  8.03 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  6.45 %
      Favored  : 90.32 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.97 (0.60), residues: 137
    helix: -1.19 (0.46), residues: 69
    sheet:  None (None), residues: 0
    loop : -2.88 (0.72), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 137 
   PHE   0.028   0.008   PHE A  45 
   TYR   0.282   0.039   TYR A 111 
   ARG   0.036   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 137 
   PHE   0.019   0.007   PHE A  67 
   TYR   0.213   0.040   TYR A 111 
   ARG   0.002   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 135  HIS
   A 137  HIS
   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  83.94 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     1
  Clashscore            =   7.66
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.84
  MolProbity score      =   2.67

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.19 %
                favored =  89.78 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     1
  Clashscore            =   3.16
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.69
  MolProbity score      =   2.05

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 128  MET  N
   A 128  MET  CA          1.46     1.55    -0.09  1.90e-02  2.41e+01   4.9*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.44     0.08  2.10e-02  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.093 (Z=  4.912)
  Mean delta:    0.016 (Z=  0.804)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   107.65    14.05  1.80e+00  6.09e+01   7.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   126.79   -15.19  2.00e+00  5.77e+01   7.6*sigma
   A 135  HIS  CA
   A 135  HIS  CB
   A 135  HIS  CG        113.80   121.14    -7.34  1.00e+00  5.39e+01   7.3*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   122.69   -12.29  1.70e+00  5.23e+01   7.2*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   134.07   -12.37  1.80e+00  4.72e+01   6.9*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   132.94   -11.24  1.80e+00  3.90e+01   6.2*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   132.45   -10.75  1.80e+00  3.57e+01   6.0*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00   127.48   -16.48  2.80e+00  3.46e+01   5.9*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   100.59     9.91  1.70e+00  3.40e+01   5.8*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   125.62    -8.72  1.50e+00  3.38e+01   5.8*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   118.33    -5.73  1.00e+00  3.28e+01   5.7*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   111.94     9.76  1.80e+00  2.94e+01   5.4*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   124.30     6.90  1.30e+00  2.82e+01   5.3*sigma
   A  82  THR  CA
   A  82  THR  CB
   A  82  THR  CG2       110.50   119.18    -8.68  1.70e+00  2.61e+01   5.1*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   118.91    -8.51  1.70e+00  2.50e+01   5.0*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N         116.20   106.26     9.94  2.00e+00  2.47e+01   5.0*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   121.43    -9.83  2.00e+00  2.41e+01   4.9*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   130.49    -8.79  1.80e+00  2.38e+01   4.9*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   116.88    -7.28  1.50e+00  2.36e+01   4.9*sigma
   A 118  ASP  C
   A 118  ASP  CA
   A 118  ASP  CB        110.10   119.24    -9.14  1.90e+00  2.32e+01   4.8*sigma
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        121.70   113.19     8.51  1.80e+00  2.24e+01   4.7*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   122.37    -8.47  1.80e+00  2.22e+01   4.7*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   117.26    -4.66  1.00e+00  2.17e+01   4.7*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.26    -4.66  1.00e+00  2.17e+01   4.7*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   103.63     7.87  1.70e+00  2.14e+01   4.6*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   130.02    -8.32  1.80e+00  2.14e+01   4.6*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   118.31    -7.81  1.70e+00  2.11e+01   4.6*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   117.38    -6.88  1.50e+00  2.11e+01   4.6*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N         116.20   107.14     9.06  2.00e+00  2.05e+01   4.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.35     5.85  1.30e+00  2.03e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.20     4.40  1.00e+00  1.93e+01   4.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O         120.80   113.34     7.46  1.70e+00  1.92e+01   4.4*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   129.57    -7.87  1.80e+00  1.91e+01   4.4*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   118.20    -8.10  1.90e+00  1.82e+01   4.3*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   116.86    -4.26  1.00e+00  1.82e+01   4.3*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG1       110.40   117.53    -7.13  1.70e+00  1.76e+01   4.2*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   107.86     8.34  2.00e+00  1.74e+01   4.2*sigma
   A 124  ALA  O
   A 124  ALA  C
   A 125  LYS  N         123.00   129.62    -6.62  1.60e+00  1.71e+01   4.1*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   117.93    -7.83  1.90e+00  1.70e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   16.481 (Z=  7.806)
  Mean delta:    2.692 (Z=  1.464)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   -83.38   -96.62  5.00e+00  3.73e+02  19.3*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00    86.05    93.95  5.00e+00  3.53e+02  18.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   -89.61   -90.39  5.00e+00  3.27e+02  18.1*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00    99.66    80.34  5.00e+00  2.58e+02  16.1*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   107.72    72.28  5.00e+00  2.09e+02  14.5*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   108.94    71.06  5.00e+00  2.02e+02  14.2*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   109.75    70.25  5.00e+00  1.97e+02  14.0*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   113.86    66.14  5.00e+00  1.75e+02  13.2*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00  -116.94   -63.06  5.00e+00  1.59e+02  12.6*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00  -119.37   -60.63  5.00e+00  1.47e+02  12.1*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -121.94   -58.06  5.00e+00  1.35e+02  11.6*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -123.79   -56.21  5.00e+00  1.26e+02  11.2*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   127.22    52.78  5.00e+00  1.11e+02  10.6*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   130.50    49.50  5.00e+00  9.80e+01   9.9*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   139.24    40.76  5.00e+00  6.65e+01   8.2*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   139.30    40.70  5.00e+00  6.62e+01   8.1*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ
   A 129  ARG  NH1         0.00   -72.08    72.08  1.00e+01  6.65e+01   7.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   144.89    35.11  5.00e+00  4.93e+01   7.0*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00   147.13    32.87  5.00e+00  4.32e+01   6.6*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -147.80   -32.20  5.00e+00  4.15e+01   6.4*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -148.65   -31.35  5.00e+00  3.93e+01   6.3*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -148.93   -31.07  5.00e+00  3.86e+01   6.2*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   149.26    30.74  5.00e+00  3.78e+01   6.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -152.61   -27.39  5.00e+00  3.00e+01   5.5*sigma
   A  46  SER  CA
   A  46  SER  C
   A  47  ASP  N
   A  47  ASP  CA        180.00   154.75    25.25  5.00e+00  2.55e+01   5.0*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   156.03    23.97  5.00e+00  2.30e+01   4.8*sigma
   A  38  ILE  CA
   A  38  ILE  C
   A  39  LEU  N
   A  39  LEU  CA        180.00   156.33    23.67  5.00e+00  2.24e+01   4.7*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   157.32    22.68  5.00e+00  2.06e+01   4.5*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -157.51   -22.49  5.00e+00  2.02e+01   4.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   158.46    21.54  5.00e+00  1.86e+01   4.3*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -159.47   -20.53  5.00e+00  1.69e+01   4.1*sigma
   A  47  ASP  CA
   A  47  ASP  C
   A  48  ALA  N
   A  48  ALA  CA        180.00   159.86    20.14  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.015
  Max. delta:   96.618
  Mean delta:   20.882

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.09     5.60  2.00e-01  7.85e+02  28.0*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.72     5.36  2.00e-01  7.20e+02  26.8*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.76     5.27  2.00e-01  6.94e+02  26.3*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.53     5.17  2.00e-01  6.69e+02  25.9*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.48     5.12  2.00e-01  6.57e+02  25.6*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -2.48     4.99  2.00e-01  6.23e+02  25.0*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.42     4.97  2.00e-01  6.18e+02  24.9*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.35     4.88  2.00e-01  5.95e+02  24.4*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.36     4.87  2.00e-01  5.92e+02  24.3*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.15     4.80  2.00e-01  5.76e+02  24.0*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -2.27     4.78  2.00e-01  5.72e+02  23.9*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -2.24     4.73  2.00e-01  5.59e+02  23.6*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -2.22     4.73  2.00e-01  5.58e+02  23.6*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.18     3.61  2.00e-01  3.26e+02  18.1*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.09     3.53  2.00e-01  3.11e+02  17.6*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -0.85     3.28  2.00e-01  2.70e+02  16.4*sigma

  Min. delta:    0.003
  Max. delta:    5.602
  Mean delta:    1.449

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O
   A 128  MET  N             0.117       0.203      138.04  10.2*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  ND1
   A 135  HIS  CD2
   A 135  HIS  CE1
   A 135  HIS  NE2           0.078       0.113       90.19   5.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O
   A  93  LEU  N             0.053       0.091       27.96   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.483
  Mean delta:    0.040

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  82  THR  HB , Angle CA-CB-HB, observed: 96.780, delta from target: 12.220
   A 126  VAL  HA , Angle C-CA-HA, observed: 95.286, delta from target: 13.714
   A 126  VAL  HB , Angle CA-CB-HB, observed: 95.157, delta from target: 13.843
   A 126  VAL  HA , Angle CB-CA-HA, observed: 122.958, delta from target: -13.958
   A 122  ILE  HA , Angle N-CA-HA, observed: 93.666, delta from target: 16.334
   A  78  ILE  HA , Angle C-CA-HA, observed: 90.416, delta from target: 18.584
   A 122  ILE  HA , Angle C-CA-HA, observed: 89.363, delta from target: 19.637
   A  51  ILE  HA , Angle CB-CA-HA, observed: 88.432, delta from target: 20.568
   A  51  ILE  HA , Angle C-CA-HA, observed: 87.920, delta from target: 21.080

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.093   2242  Z= 0.572
    Angle     :  2.420  21.080   4079  Z= 1.075
    Chirality :  1.449   5.602    176
    Planarity :  0.025   0.374    327
    Dihedral  : 17.021  96.618    769
    Min Nonbonded Distance : 1.553
  
  Molprobity Statistics.
    All-atom Clashscore : 10.37
    Ramachandran Plot:
      Outliers : 10.22 %
      Allowed  : 13.87 %
      Favored  : 75.91 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  5.65 %
      Favored  : 87.90 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 16.03 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.03 (0.58), residues: 137
    helix: -2.13 (0.49), residues: 71
    sheet:  None (None), residues: 0
    loop : -3.35 (0.65), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 135 
   PHE   0.092   0.020   PHE A  67 
   TYR   0.119   0.018   TYR A 111 
   ARG   0.352   0.039   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 135 
   PHE   0.062   0.020   PHE A  67 
   TYR   0.098   0.020   TYR A 111 
   ARG   0.007   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Ramachandran outliers =  10.22 %
                favored =  75.91 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    16
  Clashscore            =  10.37
  RMS(bonds)            =   0.0111
  RMS(angles)           =   2.42
  MolProbity score      =   2.94

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.695)
  Mean delta:    0.013 (Z=  0.671)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        121.70   134.16   -12.46  1.80e+00  4.79e+01   6.9*sigma
   A 139  HIS  CA
   A 139  HIS  CB
   A 139  HIS  CG        113.80   108.37     5.43  1.00e+00  2.94e+01   5.4*sigma
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        121.70   131.06    -9.36  1.80e+00  2.70e+01   5.2*sigma
   A 120  GLU  N
   A 120  GLU  CA
   A 120  GLU  C         111.00   124.62   -13.62  2.80e+00  2.37e+01   4.9*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   107.81     4.79  1.00e+00  2.29e+01   4.8*sigma
   A 137  HIS  N
   A 137  HIS  CA
   A 137  HIS  C         111.00   123.85   -12.85  2.80e+00  2.11e+01   4.6*sigma
   A  50  TYR  CA
   A  50  TYR  C
   A  51  ILE  N         116.20   124.92    -8.72  2.00e+00  1.90e+01   4.4*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.34     4.26  1.00e+00  1.82e+01   4.3*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   117.62    -7.22  1.70e+00  1.80e+01   4.2*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   108.39     4.21  1.00e+00  1.77e+01   4.2*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 120  GLU  O         120.80   127.66    -6.86  1.70e+00  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   13.621 (Z=  6.920)
  Mean delta:    2.079 (Z=  1.119)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   144.23    35.77  5.00e+00  5.12e+01   7.2*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -151.11   -28.89  5.00e+00  3.34e+01   5.8*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   158.95    21.05  5.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.062
  Max. delta:   88.196
  Mean delta:   18.493

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 136  HIS  CA
   A 136  HIS  N
   A 136  HIS  C
   A 136  HIS  CB          2.51    -2.35     4.86  2.00e-01  5.91e+02  24.3*sigma
   A 120  GLU  CA
   A 120  GLU  N
   A 120  GLU  C
   A 120  GLU  CB          2.51    -1.85     4.36  2.00e-01  4.76e+02  21.8*sigma

  Min. delta:    0.001
  Max. delta:    4.860
  Mean delta:    0.503

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  ND1
   A 139  HIS  CD2
   A 139  HIS  CE1
   A 139  HIS  NE2           0.059       0.100       53.03   5.0*sigma

  Min. delta:    0.000
  Max. delta:    0.072
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 120  GLU  HA , Angle N-CA-HA, observed: 97.914, delta from target: 12.086
   A 120  GLU  HA , Angle C-CA-HA, observed: 96.023, delta from target: 12.977
   A 137  HIS  HA , Angle C-CA-HA, observed: 94.968, delta from target: 14.032

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.478
    Angle     :  1.894  14.032   4079  Z= 0.831
    Chirality :  0.503   4.860    176
    Planarity :  0.013   0.065    327
    Dihedral  : 15.037  88.196    769
    Min Nonbonded Distance : 1.724
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  5.84 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  8.87 %
      Favored  : 83.87 %
    Cbeta Deviations :  3.79 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.25 (0.57), residues: 137
    helix: -1.48 (0.46), residues: 81
    sheet:  None (None), residues: 0
    loop : -3.16 (0.66), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.006   HIS A 139 
   PHE   0.072   0.021   PHE A  45 
   TYR   0.160   0.029   TYR A 111 
   ARG   0.048   0.014   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.006   HIS A 139 
   PHE   0.050   0.018   PHE A  67 
   TYR   0.137   0.033   TYR A 111 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.65    -0.20  1.90e-02  1.07e+02  10.3*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.71    -0.19  2.10e-02  7.84e+01   8.9*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.44    -0.11  1.40e-02  6.37e+01   8.0*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.57    -0.12  1.60e-02  5.56e+01   7.5*sigma
   A  93  LEU  C
   A  94  GLY  N           1.33     1.24     0.09  1.40e-02  3.83e+01   6.2*sigma
   A  79  LYS  C
   A  80  GLY  N           1.33     1.40    -0.07  1.40e-02  2.29e+01   4.8*sigma

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.196 (Z= 10.339)
  Mean delta:    0.017 (Z=  0.936)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   137.68   -26.08  2.00e+00  1.70e+02  13.0*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   136.57   -14.87  1.80e+00  6.82e+01   8.3*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  CB        111.50    97.65    13.85  1.70e+00  6.63e+01   8.1*sigma
   A  94  GLY  O
   A  94  GLY  C
   A  95  ASP  N         123.00   110.15    12.85  1.60e+00  6.45e+01   8.0*sigma
   A  93  LEU  O
   A  93  LEU  C
   A  94  GLY  N         123.00   110.57    12.43  1.60e+00  6.04e+01   7.8*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   134.60   -12.90  1.80e+00  5.13e+01   7.2*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   122.35   -11.85  1.70e+00  4.86e+01   7.0*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   130.03   -13.83  2.00e+00  4.78e+01   6.9*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00    91.74    19.26  2.80e+00  4.73e+01   6.9*sigma
   A  94  GLY  N
   A  94  GLY  CA
   A  94  GLY  C         113.30    93.57    19.73  2.90e+00  4.63e+01   6.8*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   133.48   -11.78  1.80e+00  4.28e+01   6.5*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.90   -11.20  1.80e+00  3.87e+01   6.2*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   124.97   -11.07  1.80e+00  3.78e+01   6.1*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   123.22   -11.62  2.00e+00  3.37e+01   5.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.34    -5.74  1.00e+00  3.29e+01   5.7*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   120.89   -11.79  2.20e+00  2.87e+01   5.4*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   130.90    -9.20  1.80e+00  2.61e+01   5.1*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   124.13   -10.03  2.00e+00  2.51e+01   5.0*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30    99.34     9.96  2.00e+00  2.48e+01   5.0*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   131.34    -6.94  1.40e+00  2.46e+01   5.0*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   125.85    -9.65  2.00e+00  2.33e+01   4.8*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    97.58    13.42  2.80e+00  2.30e+01   4.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  78  ILE  O         120.80   112.68     8.12  1.70e+00  2.28e+01   4.8*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O         120.80   112.81     7.99  1.70e+00  2.21e+01   4.7*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   130.12    -8.42  1.80e+00  2.19e+01   4.7*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50   103.99     7.51  1.70e+00  1.95e+01   4.4*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  93  LEU  O         120.80   128.23    -7.43  1.70e+00  1.91e+01   4.4*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  C         111.00    99.11    11.89  2.80e+00  1.80e+01   4.2*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   103.14     8.46  2.00e+00  1.79e+01   4.2*sigma
   A  52  PRO  C
   A  52  PRO  CA
   A  52  PRO  CB        110.10   117.99    -7.89  1.90e+00  1.72e+01   4.2*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG2       110.50   117.55    -7.05  1.70e+00  1.72e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.59     4.01  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   26.077 (Z= 13.039)
  Mean delta:    2.698 (Z=  1.428)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   -68.26  -111.74  5.00e+00  4.99e+02  22.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -116.09   -63.91  5.00e+00  1.63e+02  12.8*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   120.78    59.22  5.00e+00  1.40e+02  11.8*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -121.60   -58.40  5.00e+00  1.36e+02  11.7*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -123.70   -56.30  5.00e+00  1.27e+02  11.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   142.39    37.61  5.00e+00  5.66e+01   7.5*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   142.82    37.18  5.00e+00  5.53e+01   7.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -142.95   -37.05  5.00e+00  5.49e+01   7.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   144.36    35.64  5.00e+00  5.08e+01   7.1*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   156.58    23.42  5.00e+00  2.19e+01   4.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   157.16    22.84  5.00e+00  2.09e+01   4.6*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   157.94    22.06  5.00e+00  1.95e+01   4.4*sigma
   A  69  ALA  CA
   A  69  ALA  C
   A  70  LEU  N
   A  70  LEU  CA        180.00   157.94    22.06  5.00e+00  1.95e+01   4.4*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -158.09   -21.91  5.00e+00  1.92e+01   4.4*sigma

  Min. delta:    0.010
  Max. delta:  111.742
  Mean delta:   17.317

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.56     6.07  2.00e-01  9.23e+02  30.4*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.81     5.32  2.00e-01  7.09e+02  26.6*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.66     5.30  2.00e-01  7.03e+02  26.5*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -2.75     5.19  2.00e-01  6.72e+02  25.9*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  C
   A  52  PRO  CB          2.72    -2.41     5.13  2.00e-01  6.58e+02  25.7*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.33     4.84  2.00e-01  5.85e+02  24.2*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.04     4.55  2.00e-01  5.18e+02  22.8*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.00     4.52  2.00e-01  5.12e+02  22.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.76     4.19  2.00e-01  4.39e+02  21.0*sigma

  Min. delta:    0.000
  Max. delta:    6.075
  Mean delta:    1.147

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  94  GLY  CA
   A  94  GLY  C
   A  94  GLY  O
   A  95  ASP  N             0.114       0.197      129.86   9.9*sigma

  Min. delta:    0.000
  Max. delta:    0.114
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  92  THR  HB , Angle OG1-CB-HB, observed: 121.200, delta from target: -12.200
   A  78  ILE  HA , Angle CB-CA-HA, observed: 96.709, delta from target: 12.291
   A  51  ILE  HA , Angle CB-CA-HA, observed: 96.094, delta from target: 12.906
   A  77  ILE  HB , Angle CG2-CB-HB, observed: 94.398, delta from target: 14.602
   A  92  THR  HA , Angle C-CA-HA, observed: 89.736, delta from target: 19.264
   A  78  ILE  HA , Angle N-CA-HA, observed: 139.944, delta from target: -29.944

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.196   2242  Z= 0.667
    Angle     :  2.335  29.944   4079  Z= 1.034
    Chirality :  1.147   6.075    176
    Planarity :  0.013   0.114    327
    Dihedral  : 14.159 111.742    769
    Min Nonbonded Distance : 1.599
  
  Molprobity Statistics.
    All-atom Clashscore : 11.72
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  :  5.11 %
      Favored  : 86.86 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  4.84 %
      Favored  : 89.52 %
    Cbeta Deviations :  7.58 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 6.11 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.94 (0.65), residues: 137
    helix: -1.61 (0.49), residues: 75
    sheet:  None (None), residues: 0
    loop : -2.32 (0.81), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.004   HIS A 135 
   PHE   0.080   0.019   PHE A  15 
   TYR   0.180   0.020   TYR A  91 
   ARG   0.051   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.004   HIS A 135 
   PHE   0.053   0.018   PHE A  15 
   TYR   0.144   0.024   TYR A  91 
   ARG   0.004   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.92 %
                favored =  91.24 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =     5
  Clashscore            =   2.71
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.89
  MolProbity score      =   2.22

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   8.03 %
                favored =  86.86 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =    10
  Clashscore            =  11.72
  RMS(bonds)            =   0.0124
  RMS(angles)           =   2.33
  MolProbity score      =   2.78

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.54    -0.09  1.60e-02  3.35e+01   5.8*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.35     0.11  1.90e-02  3.20e+01   5.7*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.61    -0.09  2.10e-02  1.81e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.108 (Z=  5.784)
  Mean delta:    0.016 (Z=  0.820)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   136.11   -25.11  2.80e+00  8.04e+01   9.0*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   137.14   -15.44  1.80e+00  7.35e+01   8.6*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   106.29    15.41  1.80e+00  7.33e+01   8.6*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   136.91   -15.21  1.80e+00  7.14e+01   8.5*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20    99.73    16.47  2.00e+00  6.78e+01   8.2*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   134.79   -13.09  1.80e+00  5.29e+01   7.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.77   -10.87  1.50e+00  5.25e+01   7.2*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.97   -11.27  1.80e+00  3.92e+01   6.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.23   -10.53  1.80e+00  3.42e+01   5.8*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   124.21   -10.31  1.80e+00  3.28e+01   5.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  78  ILE  O         120.80   129.98    -9.18  1.70e+00  2.92e+01   5.4*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   112.10     9.60  1.80e+00  2.84e+01   5.3*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   119.35    -8.95  1.70e+00  2.77e+01   5.3*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.48    -4.88  1.00e+00  2.38e+01   4.9*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   106.52     9.68  2.00e+00  2.34e+01   4.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.25    -9.65  2.00e+00  2.33e+01   4.8*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.11     6.09  1.30e+00  2.19e+01   4.7*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   129.98    -8.28  1.80e+00  2.11e+01   4.6*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10   118.78    -8.68  1.90e+00  2.09e+01   4.6*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   130.29    -7.29  1.60e+00  2.07e+01   4.6*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   115.75     7.25  1.60e+00  2.05e+01   4.5*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   102.89     7.61  1.70e+00  2.00e+01   4.5*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   116.94    -4.34  1.00e+00  1.88e+01   4.3*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   121.59    -7.69  1.80e+00  1.82e+01   4.3*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00    99.23    11.77  2.80e+00  1.77e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.75e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   119.76    -8.16  2.00e+00  1.66e+01   4.1*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   129.04    -7.34  1.80e+00  1.66e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   25.113 (Z=  8.969)
  Mean delta:    2.557 (Z=  1.372)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -68.05  -111.95  5.00e+00  5.01e+02  22.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -105.21   -74.79  5.00e+00  2.24e+02  15.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -135.08   -44.92  5.00e+00  8.07e+01   9.0*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   136.56    43.44  5.00e+00  7.55e+01   8.7*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   138.01    41.99  5.00e+00  7.05e+01   8.4*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -138.70   -41.30  5.00e+00  6.82e+01   8.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   144.84    35.16  5.00e+00  4.94e+01   7.0*sigma
   A  71  ILE  CA
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        180.00   145.19    34.81  5.00e+00  4.85e+01   7.0*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   147.58    32.42  5.00e+00  4.20e+01   6.5*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   148.04    31.96  5.00e+00  4.09e+01   6.4*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00   153.71    26.29  5.00e+00  2.76e+01   5.3*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   154.29    25.71  5.00e+00  2.64e+01   5.1*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   154.31    25.69  5.00e+00  2.64e+01   5.1*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   157.83    22.17  5.00e+00  1.97e+01   4.4*sigma

  Min. delta:    0.013
  Max. delta:  111.953
  Mean delta:   17.430

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.40     5.04  2.00e-01  6.36e+02  25.2*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.43     4.94  2.00e-01  6.11e+02  24.7*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.39     4.90  2.00e-01  6.01e+02  24.5*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.00     3.44  2.00e-01  2.95e+02  17.2*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     0.20     2.31  2.00e-01  1.33e+02  11.5*sigma

  Min. delta:    0.001
  Max. delta:    5.044
  Mean delta:    0.731

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.048       0.083       45.73   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.059
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  78  ILE  HB , Angle CA-CB-HB, observed: 95.978, delta from target: 13.022
   A  77  ILE  HA , Angle CB-CA-HA, observed: 93.976, delta from target: 15.024
   A  51  ILE  HA , Angle CB-CA-HA, observed: 93.311, delta from target: 15.689
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.870, delta from target: 16.130
   A  89  TYR  HA , Angle C-CA-HA, observed: 82.584, delta from target: 26.416
   A  89  TYR  HA , Angle N-CA-HA, observed: 55.979, delta from target: 54.021
   A  89  TYR  HA , Angle CB-CA-HA, observed: 163.104, delta from target: -54.104

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.108   2242  Z= 0.584
    Angle     :  2.538  54.104   4079  Z= 1.073
    Chirality :  0.731   5.044    176
    Planarity :  0.010   0.062    327
    Dihedral  : 14.481 111.953    769
    Min Nonbonded Distance : 1.384
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  6.57 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  4.03 %
      Favored  : 91.13 %
    Cbeta Deviations :  4.55 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 6.87 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.96 (0.69), residues: 137
    helix: -1.51 (0.52), residues: 75
    sheet:  None (None), residues: 0
    loop : -2.51 (0.86), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A  43 
   PHE   0.039   0.011   PHE A  45 
   TYR   0.138   0.023   TYR A  91 
   ARG   0.052   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A  43 
   PHE   0.029   0.011   PHE A  45 
   TYR   0.099   0.026   TYR A  91 
   ARG   0.001   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.59    -0.14  1.90e-02  5.19e+01   7.2*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.64    -0.12  1.80e-02  4.57e+01   6.8*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.57    -0.11  1.90e-02  3.45e+01   5.9*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.40    -0.07  1.40e-02  2.40e+01   4.9*sigma
   A 125  LYS  C
   A 126  VAL  N           1.33     1.26     0.07  1.40e-02  2.22e+01   4.7*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.61    -0.09  2.10e-02  1.81e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.137 (Z=  7.202)
  Mean delta:    0.017 (Z=  0.884)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  O
   A 125  LYS  C
   A 126  VAL  N         123.00   103.94    19.06  1.60e+00  1.42e+02  11.9*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   135.15   -13.45  1.80e+00  5.58e+01   7.5*sigma
   A 139  HIS  CA
   A 139  HIS  CB
   A 139  HIS  CG        113.80   120.63    -6.83  1.00e+00  4.67e+01   6.8*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   133.46   -11.76  1.80e+00  4.27e+01   6.5*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   124.54   -12.94  2.00e+00  4.18e+01   6.5*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   125.24   -11.34  1.80e+00  3.97e+01   6.3*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   110.37    11.33  1.80e+00  3.96e+01   6.3*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   133.00   -11.30  1.80e+00  3.94e+01   6.3*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50    99.87    10.63  1.70e+00  3.91e+01   6.3*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   132.08   -10.38  1.80e+00  3.32e+01   5.8*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   131.93   -10.23  1.80e+00  3.23e+01   5.7*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   126.56   -15.56  2.80e+00  3.09e+01   5.6*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   119.80    -9.30  1.70e+00  2.99e+01   5.5*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   104.52     7.48  1.40e+00  2.85e+01   5.3*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10   120.04    -9.94  1.90e+00  2.74e+01   5.2*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   104.56     9.34  1.80e+00  2.69e+01   5.2*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40   102.63     7.77  1.50e+00  2.68e+01   5.2*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50   102.82     8.68  1.70e+00  2.61e+01   5.1*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   119.01    -8.51  1.70e+00  2.51e+01   5.0*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   118.90    -8.50  1.70e+00  2.50e+01   5.0*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   125.90    -9.70  2.00e+00  2.35e+01   4.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.34    -4.74  1.00e+00  2.25e+01   4.7*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   108.18    -5.18  1.10e+00  2.21e+01   4.7*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   130.15    -8.45  1.80e+00  2.20e+01   4.7*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   130.13    -8.43  1.80e+00  2.19e+01   4.7*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   125.50    -9.30  2.00e+00  2.16e+01   4.6*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   113.64     8.06  1.80e+00  2.01e+01   4.5*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   113.65     8.05  1.80e+00  2.00e+01   4.5*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   101.77     8.33  1.90e+00  1.92e+01   4.4*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N         116.20   107.47     8.73  2.00e+00  1.90e+01   4.4*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   107.56     8.64  2.00e+00  1.87e+01   4.3*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30   100.91     8.39  2.00e+00  1.76e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.45     4.15  1.00e+00  1.72e+01   4.2*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   129.17    -7.47  1.80e+00  1.72e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.71e+01   4.1*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   116.50     6.50  1.60e+00  1.65e+01   4.1*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   119.65    -8.05  2.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   19.060 (Z= 11.913)
  Mean delta:    2.639 (Z=  1.441)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    79.18   100.82  5.00e+00  4.07e+02  20.2*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   -83.66   -96.34  5.00e+00  3.71e+02  19.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    97.31    82.69  5.00e+00  2.73e+02  16.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   103.06    76.94  5.00e+00  2.37e+02  15.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -119.21   -60.79  5.00e+00  1.48e+02  12.2*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   120.63    59.37  5.00e+00  1.41e+02  11.9*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   122.88    57.12  5.00e+00  1.30e+02  11.4*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -124.97   -55.03  5.00e+00  1.21e+02  11.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   130.97    49.03  5.00e+00  9.62e+01   9.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -132.11   -47.89  5.00e+00  9.17e+01   9.6*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -142.80   -37.20  5.00e+00  5.54e+01   7.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -151.55   -28.45  5.00e+00  3.24e+01   5.7*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   152.15    27.85  5.00e+00  3.10e+01   5.6*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00  -152.96   -27.04  5.00e+00  2.92e+01   5.4*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -153.61   -26.39  5.00e+00  2.79e+01   5.3*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -154.67   -25.33  5.00e+00  2.57e+01   5.1*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -156.38   -23.62  5.00e+00  2.23e+01   4.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   156.40    23.60  5.00e+00  2.23e+01   4.7*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00  -157.80   -22.20  5.00e+00  1.97e+01   4.4*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   159.84    20.16  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.009
  Max. delta:  100.818
  Mean delta:   18.797

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.23     5.74  2.00e-01  8.24e+02  28.7*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.98     5.50  2.00e-01  7.55e+02  27.5*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.75     5.19  2.00e-01  6.72e+02  25.9*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.54     5.19  2.00e-01  6.72e+02  25.9*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -2.63     5.11  2.00e-01  6.53e+02  25.6*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.33     4.77  2.00e-01  5.70e+02  23.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.67     4.11  2.00e-01  4.22e+02  20.5*sigma

  Min. delta:    0.001
  Max. delta:    5.743
  Mean delta:    1.032

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.265       0.275     1405.84  13.7*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.105       0.185      219.31   9.3*sigma
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CD            0.143       0.248       32.94   5.0*sigma

  Min. delta:    0.000
  Max. delta:    0.265
  Mean delta:    0.028

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  51  ILE  HA , Angle C-CA-HA, observed: 96.401, delta from target: 12.599
   A  89  TYR  HA , Angle N-CA-HA, observed: 96.472, delta from target: 13.528
   A  78  ILE  HA , Angle CB-CA-HA, observed: 94.950, delta from target: 14.050
   A  81  TYR  HA , Angle C-CA-HA, observed: 94.688, delta from target: 14.312
   A  89  TYR  HA , Angle CB-CA-HA, observed: 123.577, delta from target: -14.577
   A  51  ILE  HA , Angle CB-CA-HA, observed: 93.818, delta from target: 15.182

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.137   2242  Z= 0.629
    Angle     :  2.303  19.060   4079  Z= 1.040
    Chirality :  1.032   5.743    176
    Planarity :  0.021   0.266    327
    Dihedral  : 15.604 100.818    769
    Min Nonbonded Distance : 1.748
  
  Molprobity Statistics.
    All-atom Clashscore : 9.02
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  : 10.22 %
      Favored  : 81.75 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  7.26 %
      Favored  : 86.29 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 7.63 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.58 (0.63), residues: 137
    helix: -2.25 (0.55), residues: 68
    sheet:  None (None), residues: 0
    loop : -2.49 (0.69), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.040   0.012   PHE A  67 
   TYR   0.605   0.053   TYR A  91 
   ARG   0.057   0.006   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.028   0.012   PHE A  67 
   TYR   0.500   0.060   TYR A  91 
   ARG   0.004   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 139  HIS

=================================== Summary ===================================

  Ramachandran outliers =   3.65 %
                favored =  89.78 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     6
  Clashscore            =   6.76
  RMS(bonds)            =   0.0111
  RMS(angles)           =   2.54
  MolProbity score      =   2.45

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Ramachandran outliers =   8.03 %
                favored =  81.75 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    14
  Clashscore            =   9.02
  RMS(bonds)            =   0.0119
  RMS(angles)           =   2.30
  MolProbity score      =   2.81

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.074 (Z=  3.512)
  Mean delta:    0.014 (Z=  0.734)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   135.84   -14.14  1.80e+00  6.17e+01   7.9*sigma
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG1       110.40   121.41   -11.01  1.70e+00  4.19e+01   6.5*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   123.96   -12.36  2.00e+00  3.82e+01   6.2*sigma
   A  86  ILE  N
   A  86  ILE  CA
   A  86  ILE  CB        111.50   121.91   -10.41  1.70e+00  3.75e+01   6.1*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   132.56   -10.86  1.80e+00  3.64e+01   6.0*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.55   -10.85  1.80e+00  3.63e+01   6.0*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   123.26   -11.66  2.00e+00  3.40e+01   5.8*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   103.90     8.10  1.40e+00  3.35e+01   5.8*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   126.26   -15.26  2.80e+00  2.97e+01   5.5*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   117.62    -8.02  1.50e+00  2.86e+01   5.3*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.58     5.02  1.00e+00  2.52e+01   5.0*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   113.15     8.55  1.80e+00  2.26e+01   4.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.35    -4.75  1.00e+00  2.25e+01   4.7*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   130.22    -8.52  1.80e+00  2.24e+01   4.7*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   106.74     9.46  2.00e+00  2.24e+01   4.7*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   108.19    -5.19  1.10e+00  2.23e+01   4.7*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   119.03    -8.93  1.90e+00  2.21e+01   4.7*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  C         111.00   124.08   -13.08  2.80e+00  2.18e+01   4.7*sigma
   A  83  THR  CA
   A  83  THR  CB
   A  83  THR  CG2       110.50   118.39    -7.89  1.70e+00  2.15e+01   4.6*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD2       110.70   124.26   -13.56  3.00e+00  2.04e+01   4.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.41     5.79  1.30e+00  1.98e+01   4.5*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   129.66    -7.96  1.80e+00  1.96e+01   4.4*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.83     5.37  1.30e+00  1.71e+01   4.1*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   103.48     7.02  1.70e+00  1.71e+01   4.1*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   129.13    -7.43  1.80e+00  1.70e+01   4.1*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   128.97    -7.27  1.80e+00  1.63e+01   4.0*sigma
   A 108  ILE  C
   A 108  ILE  CA
   A 108  ILE  CB        111.60   119.67    -8.07  2.00e+00  1.63e+01   4.0*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   117.35    -6.85  1.70e+00  1.62e+01   4.0*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.58     4.02  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   15.264 (Z=  7.854)
  Mean delta:    2.516 (Z=  1.357)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -110.73   -69.27  5.00e+00  1.92e+02  13.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -120.83   -59.17  5.00e+00  1.40e+02  11.8*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   124.34    55.66  5.00e+00  1.24e+02  11.1*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   125.30    54.70  5.00e+00  1.20e+02  10.9*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00  -130.32   -49.68  5.00e+00  9.87e+01   9.9*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -136.12   -43.88  5.00e+00  7.70e+01   8.8*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   141.20    38.80  5.00e+00  6.02e+01   7.8*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   147.43    32.57  5.00e+00  4.24e+01   6.5*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   147.55    32.45  5.00e+00  4.21e+01   6.5*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   147.74    32.26  5.00e+00  4.16e+01   6.5*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   147.74    32.26  5.00e+00  4.16e+01   6.5*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -147.92   -32.08  5.00e+00  4.12e+01   6.4*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA          0.00   -32.00    32.00  5.00e+00  4.10e+01   6.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA          0.00    30.45   -30.45  5.00e+00  3.71e+01   6.1*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -149.72   -30.28  5.00e+00  3.67e+01   6.1*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00  -150.98   -29.02  5.00e+00  3.37e+01   5.8*sigma
   A 108  ILE  CA
   A 108  ILE  C
   A 109  LYS  N
   A 109  LYS  CA        180.00  -151.25   -28.75  5.00e+00  3.31e+01   5.7*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00  -151.95   -28.05  5.00e+00  3.15e+01   5.6*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -152.69   -27.31  5.00e+00  2.98e+01   5.5*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   153.11    26.89  5.00e+00  2.89e+01   5.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -155.29   -24.71  5.00e+00  2.44e+01   4.9*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   155.88    24.12  5.00e+00  2.33e+01   4.8*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   156.37    23.63  5.00e+00  2.23e+01   4.7*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   157.96    22.04  5.00e+00  1.94e+01   4.4*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   158.00    22.00  5.00e+00  1.94e+01   4.4*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00   158.50    21.50  5.00e+00  1.85e+01   4.3*sigma
   A 111  TYR  CA
   A 111  TYR  C
   A 112  VAL  N
   A 112  VAL  CA        180.00   159.13    20.87  5.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.002
  Max. delta:   86.857
  Mean delta:   17.508

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.78     5.31  2.00e-01  7.05e+02  26.5*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.64     5.28  2.00e-01  6.98e+02  26.4*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.71     5.22  2.00e-01  6.82e+02  26.1*sigma
   A 118  ASP  CA
   A 118  ASP  N
   A 118  ASP  C
   A 118  ASP  CB          2.51    -2.22     4.73  2.00e-01  5.59e+02  23.6*sigma
   A 132  LEU  CA
   A 132  LEU  N
   A 132  LEU  C
   A 132  LEU  CB          2.51    -2.21     4.72  2.00e-01  5.56e+02  23.6*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -2.12     4.56  2.00e-01  5.19e+02  22.8*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -1.84     4.35  2.00e-01  4.73e+02  21.7*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.66     4.09  2.00e-01  4.18e+02  20.5*sigma
   A 108  ILE  CA
   A 108  ILE  N
   A 108  ILE  C
   A 108  ILE  CB          2.43    -1.29     3.73  2.00e-01  3.47e+02  18.6*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.11     3.54  2.00e-01  3.14e+02  17.7*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     0.68     1.83  2.00e-01  8.35e+01   9.1*sigma
   A  86  ILE  CA
   A  86  ILE  N
   A  86  ILE  C
   A  86  ILE  CB          2.43     1.29     1.14  2.00e-01  3.26e+01   5.7*sigma

  Min. delta:    0.000
  Max. delta:    5.309
  Mean delta:    1.118

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.078       0.135      123.07   6.8*sigma
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.099       0.119      170.66   5.9*sigma

  Min. delta:    0.000
  Max. delta:    0.147
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  51  ILE  HA , Angle C-CA-HA, observed: 95.962, delta from target: 13.038
   A  74  ASP  HA , Angle C-CA-HA, observed: 95.338, delta from target: 13.662
   A  51  ILE  HA , Angle CB-CA-HA, observed: 94.759, delta from target: 14.241
   A  93  LEU  HG , Angle CB-CG-HG, observed: 94.548, delta from target: 14.452
   A 108  ILE  HA , Angle C-CA-HA, observed: 94.014, delta from target: 14.986
   A  78  ILE  HA , Angle CB-CA-HA, observed: 93.054, delta from target: 15.946
   A  89  TYR  HA , Angle N-CA-HA, observed: 92.525, delta from target: 17.475
   A  78  ILE  HA , Angle C-CA-HA, observed: 90.281, delta from target: 18.719
   A  97  SER  HA , Angle C-CA-HA, observed: 87.840, delta from target: 21.160
   A  86  ILE  HA , Angle N-CA-HA, observed: 88.762, delta from target: 21.238
   A  97  SER  HA , Angle N-CA-HA, observed: 85.466, delta from target: 24.534

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.074   2242  Z= 0.522
    Angle     :  2.349  24.534   4079  Z= 1.021
    Chirality :  1.118   5.309    176
    Planarity :  0.016   0.147    327
    Dihedral  : 14.594  86.857    769
    Min Nonbonded Distance : 1.662
  
  Molprobity Statistics.
    All-atom Clashscore : 10.82
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  :  8.03 %
      Favored  : 85.40 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  3.23 %
      Favored  : 90.32 %
    Cbeta Deviations : 12.88 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 10.69 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.99 (0.64), residues: 137
    helix: -1.34 (0.49), residues: 78
    sheet:  None (None), residues: 0
    loop : -2.86 (0.78), residues: 59
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A 138 
   PHE   0.235   0.035   PHE A  15 
   TYR   0.160   0.026   TYR A  12 
   ARG   0.044   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A 138 
   PHE   0.156   0.035   PHE A  15 
   TYR   0.135   0.027   TYR A  12 
   ARG   0.005   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   6.57 %
                favored =  85.40 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    17
  Clashscore            =  10.82
  RMS(bonds)            =   0.0101
  RMS(angles)           =   2.35
  MolProbity score      =   2.82

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.583)
  Mean delta:    0.001 (Z=  0.064)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.622 (Z=  1.404)
  Mean delta:    0.376 (Z=  0.206)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   83.106
  Mean delta:   23.693

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.096
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.046
    Angle     :  0.979   4.827   4077  Z= 0.342
    Chirality :  0.035   0.096    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.502  83.106    768
    Min Nonbonded Distance : 1.620
  
  Molprobity Statistics.
    All-atom Clashscore : 19.85
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  : 18.25 %
      Favored  : 75.91 %
    Rotamer:
      Outliers : 22.58 %
      Allowed  : 20.97 %
      Favored  : 56.45 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.55 (0.42), residues: 137
    helix: -4.17 (0.32), residues: 60
    sheet:  None (None), residues: 0
    loop : -4.73 (0.47), residues: 77
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.002   0.001   PHE A  15 
   TYR   0.002   0.001   TYR A  68 
   ARG   0.000   0.000   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A  12 
   ARG   0.000   0.000   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   5.84 %
                favored =  75.91 %
  Rotamer outliers      =  22.58 %
  C-beta deviations     =     0
  Clashscore            =  19.85
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.61

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  2.854)
  Mean delta:    0.013 (Z=  0.667)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   136.24   -14.54  1.80e+00  6.52e+01   8.1*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   109.96    11.74  1.80e+00  4.25e+01   6.5*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   120.72   -10.62  1.90e+00  3.13e+01   5.6*sigma
   A  84  GLU  O
   A  84  GLU  C
   A  85  LYS  N         123.00   115.00     8.00  1.60e+00  2.50e+01   5.0*sigma
   A  99  LEU  N
   A  99  LEU  CA
   A  99  LEU  CB        110.50   118.38    -7.88  1.70e+00  2.15e+01   4.6*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   102.96     8.64  2.00e+00  1.87e+01   4.3*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N         116.20   107.58     8.62  2.00e+00  1.86e+01   4.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   107.80     8.40  2.00e+00  1.76e+01   4.2*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma
   A 131  ILE  O
   A 131  ILE  C
   A 132  LEU  N         123.00   129.69    -6.69  1.60e+00  1.75e+01   4.2*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   108.57     4.03  1.00e+00  1.62e+01   4.0*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.99     5.21  1.30e+00  1.61e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:   14.535 (Z=  8.075)
  Mean delta:    2.259 (Z=  1.224)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00   117.28    62.72  5.00e+00  1.57e+02  12.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   134.65    45.35  5.00e+00  8.23e+01   9.1*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   146.06    33.94  5.00e+00  4.61e+01   6.8*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -152.57   -27.43  5.00e+00  3.01e+01   5.5*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   153.22    26.78  5.00e+00  2.87e+01   5.4*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -156.14   -23.86  5.00e+00  2.28e+01   4.8*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   159.21    20.79  5.00e+00  1.73e+01   4.2*sigma

  Min. delta:    0.035
  Max. delta:   92.450
  Mean delta:   17.540

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51    -2.09     4.60  2.00e-01  5.30e+02  23.0*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.66     4.17  2.00e-01  4.35e+02  20.9*sigma
   A 132  LEU  CA
   A 132  LEU  N
   A 132  LEU  C
   A 132  LEU  CB          2.51    -1.55     4.06  2.00e-01  4.12e+02  20.3*sigma
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51    -1.01     3.52  2.00e-01  3.10e+02  17.6*sigma

  Min. delta:    0.001
  Max. delta:    4.603
  Mean delta:    0.628

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.109       0.200      236.84  10.0*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.061       0.104       74.53   5.2*sigma
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.061       0.094       64.49   4.7*sigma

  Min. delta:    0.000
  Max. delta:    0.118
  Mean delta:    0.021

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  99  LEU  HA , Angle C-CA-HA, observed: 95.577, delta from target: 13.423
   A  89  TYR  HA , Angle C-CA-HA, observed: 93.209, delta from target: 15.791
   A  99  LEU  HA , Angle CB-CA-HA, observed: 92.354, delta from target: 16.646

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2242  Z= 0.475
    Angle     :  2.022  16.646   4079  Z= 0.897
    Chirality :  0.628   4.603    176
    Planarity :  0.015   0.100    327
    Dihedral  : 14.829  92.450    769
    Min Nonbonded Distance : 1.643
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  8.76 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  4.03 %
      Favored  : 91.94 %
    Cbeta Deviations :  3.79 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.64 (0.66), residues: 137
    helix: -0.86 (0.57), residues: 57
    sheet:  None (None), residues: 0
    loop : -2.56 (0.70), residues: 80
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.006   HIS A 138 
   PHE   0.165   0.044   PHE A  67 
   TYR   0.233   0.032   TYR A  50 
   ARG   0.096   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.006   HIS A 138 
   PHE   0.113   0.046   PHE A  67 
   TYR   0.200   0.037   TYR A  50 
   ARG   0.008   0.003   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  89.78 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     5
  Clashscore            =   5.86
  RMS(bonds)            =   0.0092
  RMS(angles)           =   2.02
  MolProbity score      =   2.34

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.566)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.615 (Z=  1.363)
  Mean delta:    0.377 (Z=  0.206)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   88.915
  Mean delta:   24.135

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.095
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.045
    Angle     :  0.980   4.834   4077  Z= 0.342
    Chirality :  0.035   0.095    176
    Planarity :  0.000   0.002    326
    Dihedral  : 18.725  88.915    768
    Min Nonbonded Distance : 1.319
  
  Molprobity Statistics.
    All-atom Clashscore : 18.04
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  : 15.33 %
      Favored  : 78.10 %
    Rotamer:
      Outliers : 25.81 %
      Allowed  : 18.55 %
      Favored  : 55.65 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.69 (0.43), residues: 137
    helix: -3.91 (0.41), residues: 64
    sheet:  None (None), residues: 0
    loop : -5.18 (0.44), residues: 73
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.002   0.001   PHE A  15 
   TYR   0.003   0.001   TYR A  68 
   ARG   0.001   0.000   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A  68 
   ARG   0.001   0.000   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  72  ASN

=================================== Summary ===================================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.774)
  Mean delta:    0.013 (Z=  0.671)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   134.91   -13.21  1.80e+00  5.39e+01   7.3*sigma
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   120.15    -6.35  1.00e+00  4.04e+01   6.4*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N         116.20   105.11    11.09  2.00e+00  3.08e+01   5.5*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.29     4.31  1.00e+00  1.86e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.45     4.15  1.00e+00  1.73e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   13.215 (Z=  7.341)
  Mean delta:    1.959 (Z=  1.088)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  46  SER  CA
   A  46  SER  C
   A  47  ASP  N
   A  47  ASP  CA        180.00  -141.30   -38.70  5.00e+00  5.99e+01   7.7*sigma

  Min. delta:    0.088
  Max. delta:   88.271
  Mean delta:   17.036

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51    -1.97     4.48  2.00e-01  5.02e+02  22.4*sigma

  Min. delta:    0.000
  Max. delta:    4.482
  Mean delta:    0.354

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.078       0.151      120.54   7.5*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.118       0.103      278.37   5.1*sigma

  Min. delta:    0.000
  Max. delta:    0.118
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.478
    Angle     :  1.773  13.215   4079  Z= 0.797
    Chirality :  0.354   4.482    176
    Planarity :  0.014   0.114    327
    Dihedral  : 14.785  88.271    769
    Min Nonbonded Distance : 1.774
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.03 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.70 (0.64), residues: 137
    helix:  0.07 (0.56), residues: 57
    sheet:  None (None), residues: 0
    loop : -2.15 (0.67), residues: 80
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.007   HIS A 137 
   PHE   0.042   0.013   PHE A  45 
   TYR   0.247   0.040   TYR A  50 
   ARG   0.072   0.015   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.007   HIS A 137 
   PHE   0.025   0.010   PHE A  15 
   TYR   0.202   0.041   TYR A  50 
   ARG   0.008   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 136  HIS

=================================== Summary ===================================

  Ramachandran outliers =   6.57 %
                favored =  78.10 %
  Rotamer outliers      =  25.81 %
  C-beta deviations     =     0
  Clashscore            =  18.04
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.59

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  94.16 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     1
  Clashscore            =   4.51
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.77
  MolProbity score      =   1.91

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.719)
  Mean delta:    0.013 (Z=  0.667)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   117.51    -4.91  1.00e+00  2.41e+01   4.9*sigma
   A  84  GLU  CA
   A  84  GLU  CB
   A  84  GLU  CG        114.10   123.63    -9.53  2.00e+00  2.27e+01   4.8*sigma
   A  72  ASN  OD1
   A  72  ASN  CG
   A  72  ASN  ND2       122.60   117.96     4.64  1.00e+00  2.15e+01   4.6*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.81     5.39  1.30e+00  1.72e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    9.532 (Z=  4.911)
  Mean delta:    1.949 (Z=  1.064)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   158.63    21.37  5.00e+00  1.83e+01   4.3*sigma

  Min. delta:    0.008
  Max. delta:   87.961
  Mean delta:   16.423

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.398
  Mean delta:    0.107

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.118       0.208      277.98  10.4*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.060       0.117       70.91   5.9*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.056       0.105       63.27   5.3*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  ND1
   A  43  HIS  CD2
   A  43  HIS  CE1
   A  43  HIS  NE2           0.059       0.083       51.98   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.118
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.475
    Angle     :  1.794   9.532   4079  Z= 0.791
    Chirality :  0.107   0.398    176
    Planarity :  0.013   0.116    327
    Dihedral  : 13.575  87.961    769
    Min Nonbonded Distance : 1.730
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  5.11 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.03 %
      Favored  : 93.55 %
    Cbeta Deviations :  2.27 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.39 (0.64), residues: 137
    helix: -0.72 (0.60), residues: 62
    sheet:  None (None), residues: 0
    loop : -1.05 (0.66), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.006   HIS A 138 
   PHE   0.062   0.018   PHE A  15 
   TYR   0.256   0.034   TYR A  91 
   ARG   0.052   0.011   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.006   HIS A 138 
   PHE   0.039   0.016   PHE A  15 
   TYR   0.208   0.040   TYR A  91 
   ARG   0.006   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Ramachandran outliers =   2.92 %
                favored =  91.97 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     3
  Clashscore            =   0.90
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.79
  MolProbity score      =   1.55

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.62    -0.10  2.10e-02  2.23e+01   4.7*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.099 (Z=  4.724)
  Mean delta:    0.015 (Z=  0.747)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   142.91   -21.21  1.80e+00  1.39e+02  11.8*sigma
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   137.59   -15.89  1.80e+00  7.80e+01   8.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   100.59    15.61  2.00e+00  6.09e+01   7.8*sigma
   A  93  LEU  CD1
   A  93  LEU  CG
   A  93  LEU  CD2       110.80   127.91   -17.11  2.20e+00  6.05e+01   7.8*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   111.12    11.88  1.60e+00  5.52e+01   7.4*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   122.04   -11.64  1.70e+00  4.69e+01   6.8*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   121.72   -11.22  1.70e+00  4.36e+01   6.6*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   133.21   -11.51  1.80e+00  4.09e+01   6.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   128.66   -12.46  2.00e+00  3.88e+01   6.2*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   123.88   -12.28  2.00e+00  3.77e+01   6.1*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   132.31   -10.61  1.80e+00  3.47e+01   5.9*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N         116.20   104.61    11.59  2.00e+00  3.36e+01   5.8*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   132.08   -10.38  1.80e+00  3.33e+01   5.8*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   104.00     8.00  1.40e+00  3.26e+01   5.7*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  CB        110.50   101.08     9.42  1.70e+00  3.07e+01   5.5*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   117.91    -8.31  1.50e+00  3.07e+01   5.5*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   129.85    -9.05  1.70e+00  2.83e+01   5.3*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   131.21    -9.51  1.80e+00  2.79e+01   5.3*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.01    -9.31  1.80e+00  2.67e+01   5.2*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.60    -5.00  1.00e+00  2.50e+01   5.0*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   130.61    -8.91  1.80e+00  2.45e+01   5.0*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   118.70    -8.30  1.70e+00  2.39e+01   4.9*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   108.35    -5.35  1.10e+00  2.36e+01   4.9*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   130.44    -8.74  1.80e+00  2.36e+01   4.9*sigma
   A  92  THR  O
   A  92  THR  C
   A  93  LEU  N         123.00   115.34     7.66  1.60e+00  2.29e+01   4.8*sigma
   A 129  ARG  C
   A 129  ARG  CA
   A 129  ARG  CB        110.10   118.83    -8.73  1.90e+00  2.11e+01   4.6*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   118.80    -8.70  1.90e+00  2.09e+01   4.6*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   129.53    -7.83  1.80e+00  1.89e+01   4.3*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.57     5.63  1.30e+00  1.87e+01   4.3*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   101.97     8.13  1.90e+00  1.83e+01   4.3*sigma
   A  99  LEU  N
   A  99  LEU  CA
   A  99  LEU  C         111.00    99.15    11.85  2.80e+00  1.79e+01   4.2*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  86  ILE  O         120.80   127.79    -6.99  1.70e+00  1.69e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   108.11     8.09  2.00e+00  1.63e+01   4.0*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.98     5.22  1.30e+00  1.61e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:   21.212 (Z= 11.785)
  Mean delta:    2.681 (Z=  1.456)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    47.02   132.98  5.00e+00  7.07e+02  26.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -101.37   -78.63  5.00e+00  2.47e+02  15.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   116.33    63.67  5.00e+00  1.62e+02  12.7*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   119.22    60.78  5.00e+00  1.48e+02  12.2*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00  -122.96   -57.04  5.00e+00  1.30e+02  11.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -125.13   -54.87  5.00e+00  1.20e+02  11.0*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   129.00    51.00  5.00e+00  1.04e+02  10.2*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -134.55   -45.45  5.00e+00  8.26e+01   9.1*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -147.26   -32.74  5.00e+00  4.29e+01   6.5*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   148.50    31.50  5.00e+00  3.97e+01   6.3*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   150.39    29.61  5.00e+00  3.51e+01   5.9*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   152.45    27.55  5.00e+00  3.04e+01   5.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA          0.00   -27.08    27.08  5.00e+00  2.93e+01   5.4*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -153.02   -26.98  5.00e+00  2.91e+01   5.4*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   155.46    24.54  5.00e+00  2.41e+01   4.9*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   158.13    21.87  5.00e+00  1.91e+01   4.4*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   158.91    21.09  5.00e+00  1.78e+01   4.2*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   159.91    20.09  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.035
  Max. delta:  132.979
  Mean delta:   17.664

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -3.09     5.61  2.00e-01  7.86e+02  28.0*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.59     5.24  2.00e-01  6.86e+02  26.2*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.71     5.23  2.00e-01  6.85e+02  26.2*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.69     5.20  2.00e-01  6.77e+02  26.0*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -2.75     5.18  2.00e-01  6.71e+02  25.9*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.65     5.16  2.00e-01  6.66e+02  25.8*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.53     5.04  2.00e-01  6.36e+02  25.2*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -1.98     4.53  2.00e-01  5.14e+02  22.7*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.83     4.26  2.00e-01  4.55e+02  21.3*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.55     4.06  2.00e-01  4.12e+02  20.3*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43     1.43     1.00  2.00e-01  2.51e+01   5.0*sigma
   A 126  VAL  CB
   A 126  VAL  CA
   A 126  VAL  CG1
   A 126  VAL  CG2        -2.63    -1.72    -0.91  2.00e-01  2.05e+01   4.5*sigma
   A 129  ARG  CA
   A 129  ARG  N
   A 129  ARG  C
   A 129  ARG  CB          2.51     1.61     0.91  2.00e-01  2.05e+01   4.5*sigma

  Min. delta:    0.001
  Max. delta:    5.605
  Mean delta:    1.201

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.063       0.114       80.46   5.7*sigma

  Min. delta:    0.000
  Max. delta:    0.147
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="SER A  90  conformer  : H 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  89  TYR  HA , Angle C-CA-HA, observed: 96.655, delta from target: 12.345
   A  51  ILE  HA , Angle CB-CA-HA, observed: 95.625, delta from target: 13.375
   A 129  ARG  HA , Angle C-CA-HA, observed: 95.108, delta from target: 13.892
   A  93  LEU  HG , Angle CD1-CG-HG, observed: 92.268, delta from target: 15.732
   A  78  ILE  HA , Angle C-CA-HA, observed: 92.584, delta from target: 16.416
   A 126  VAL  HB , Angle CA-CB-HB, observed: 89.001, delta from target: 19.999

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.099   2241  Z= 0.532
    Angle     :  2.336  21.212   4077  Z= 1.051
    Chirality :  1.201   5.605    176
    Planarity :  0.014   0.147    326
    Dihedral  : 14.322 132.979    768
    Min Nonbonded Distance : 1.614
  
  Molprobity Statistics.
    All-atom Clashscore : 17.14
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  : 11.68 %
      Favored  : 82.48 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  6.45 %
      Favored  : 88.71 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 6.87 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.54 (0.59), residues: 137
    helix: -1.65 (0.55), residues: 63
    sheet:  None (None), residues: 0
    loop : -3.10 (0.59), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A  43 
   PHE   0.104   0.021   PHE A  15 
   TYR   0.138   0.021   TYR A  12 
   ARG   0.024   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A  43 
   PHE   0.071   0.019   PHE A  15 
   TYR   0.114   0.024   TYR A  12 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.62    -0.17  1.90e-02  7.57e+01   8.7*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.42    -0.10  1.40e-02  4.66e+01   6.8*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.65    -0.12  2.10e-02  3.46e+01   5.9*sigma
   A  92  THR  N
   A  92  THR  CA          1.46     1.56    -0.10  1.90e-02  2.97e+01   5.5*sigma
   A  79  LYS  C
   A  80  GLY  N           1.33     1.27     0.06  1.40e-02  1.90e+01   4.4*sigma
   A  92  THR  CB
   A  92  THR  OG1         1.43     1.36     0.07  1.60e-02  1.88e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.165 (Z=  8.703)
  Mean delta:    0.018 (Z=  0.925)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   135.81   -25.31  1.70e+00  2.22e+02  14.9*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   106.28    15.42  1.80e+00  7.34e+01   8.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20    99.39    16.81  2.00e+00  7.06e+01   8.4*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   128.37   -16.77  2.00e+00  7.03e+01   8.4*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   135.98   -14.28  1.80e+00  6.29e+01   7.9*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   135.57   -13.87  1.80e+00  5.93e+01   7.7*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.21   -11.31  1.50e+00  5.69e+01   7.5*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  C         111.00   130.94   -19.94  2.80e+00  5.07e+01   7.1*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00   128.52   -17.52  2.80e+00  3.91e+01   6.3*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   103.85    12.35  2.00e+00  3.81e+01   6.2*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.40   -10.70  1.80e+00  3.54e+01   5.9*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.43    -9.73  1.80e+00  2.92e+01   5.4*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   122.40   -10.80  2.00e+00  2.92e+01   5.4*sigma
   A  84  GLU  C
   A  84  GLU  CA
   A  84  GLU  CB        110.10   120.13   -10.03  1.90e+00  2.79e+01   5.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   129.70    -8.90  1.70e+00  2.74e+01   5.2*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.72   -10.12  2.00e+00  2.56e+01   5.1*sigma
   A  98  SER  C
   A  98  SER  CA
   A  98  SER  CB        110.10   119.66    -9.56  1.90e+00  2.53e+01   5.0*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   112.76     8.94  1.80e+00  2.47e+01   5.0*sigma
   A  95  ASP  C
   A  95  ASP  CA
   A  95  ASP  CB        110.10   119.39    -9.29  1.90e+00  2.39e+01   4.9*sigma
   A 126  VAL  O
   A 126  VAL  C
   A 127  ARG  N         123.00   130.78    -7.78  1.60e+00  2.37e+01   4.9*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   125.89    -9.69  2.00e+00  2.35e+01   4.8*sigma
   A  80  GLY  N
   A  80  GLY  CA
   A  80  GLY  C         113.30    99.26    14.04  2.90e+00  2.34e+01   4.8*sigma
   A  97  SER  CA
   A  97  SER  C
   A  97  SER  O         120.80   128.88    -8.08  1.70e+00  2.26e+01   4.8*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   118.79    -8.69  1.90e+00  2.09e+01   4.6*sigma
   A  93  LEU  O
   A  93  LEU  C
   A  94  GLY  N         123.00   115.76     7.24  1.60e+00  2.05e+01   4.5*sigma
   A  88  ASP  C
   A  88  ASP  CA
   A  88  ASP  CB        110.10   118.66    -8.56  1.90e+00  2.03e+01   4.5*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   107.20     9.00  2.00e+00  2.02e+01   4.5*sigma
   A 100  GLN  CB
   A 100  GLN  CG
   A 100  GLN  CD        112.60   120.14    -7.54  1.70e+00  1.97e+01   4.4*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00   123.21   -12.21  2.80e+00  1.90e+01   4.4*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   129.52    -7.82  1.80e+00  1.89e+01   4.3*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   116.93    -4.33  1.00e+00  1.87e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.30     4.30  1.00e+00  1.85e+01   4.3*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   116.78    -4.18  1.00e+00  1.75e+01   4.2*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   129.22    -7.52  1.80e+00  1.75e+01   4.2*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   117.46    -7.06  1.70e+00  1.73e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.45     4.15  1.00e+00  1.72e+01   4.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O         120.80   127.68    -6.88  1.70e+00  1.64e+01   4.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   114.00     6.80  1.70e+00  1.60e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   25.306 (Z= 14.886)
  Mean delta:    2.825 (Z=  1.494)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00    71.11   108.89  5.00e+00  4.74e+02  21.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00    74.34   105.66  5.00e+00  4.47e+02  21.1*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00    84.70    95.30  5.00e+00  3.63e+02  19.1*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    91.21    88.79  5.00e+00  3.15e+02  17.8*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   -96.30   -83.70  5.00e+00  2.80e+02  16.7*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -104.24   -75.76  5.00e+00  2.30e+02  15.2*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   109.15    70.85  5.00e+00  2.01e+02  14.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -115.39   -64.61  5.00e+00  1.67e+02  12.9*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -121.47   -58.53  5.00e+00  1.37e+02  11.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   137.38    42.62  5.00e+00  7.27e+01   8.5*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   139.09    40.91  5.00e+00  6.69e+01   8.2*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   140.08    39.92  5.00e+00  6.37e+01   8.0*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -141.15   -38.85  5.00e+00  6.04e+01   7.8*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   155.56    24.44  5.00e+00  2.39e+01   4.9*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   156.02    23.98  5.00e+00  2.30e+01   4.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   158.50    21.50  5.00e+00  1.85e+01   4.3*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   159.34    20.66  5.00e+00  1.71e+01   4.1*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -159.89   -20.11  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.020
  Max. delta:  108.895
  Mean delta:   19.280

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.48     5.03  2.00e-01  6.32e+02  25.1*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.37     4.88  2.00e-01  5.94e+02  24.4*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51    -2.34     4.85  2.00e-01  5.87e+02  24.2*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -2.31     4.82  2.00e-01  5.81e+02  24.1*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.16     4.67  2.00e-01  5.46e+02  23.4*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.05     4.56  2.00e-01  5.21e+02  22.8*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.10     4.55  2.00e-01  5.16e+02  22.7*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -1.86     4.38  2.00e-01  4.81e+02  21.9*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -1.61     4.12  2.00e-01  4.24e+02  20.6*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -1.04     3.48  2.00e-01  3.02e+02  17.4*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -0.78     3.42  2.00e-01  2.93e+02  17.1*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.93     3.36  2.00e-01  2.83e+02  16.8*sigma
   A  83  THR  CA
   A  83  THR  N
   A  83  THR  C
   A  83  THR  CB          2.53     1.67     0.85  2.00e-01  1.81e+01   4.3*sigma

  Min. delta:    0.001
  Max. delta:    5.029
  Mean delta:    1.156

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.075       0.141      113.62   7.1*sigma
   A  67  PHE  CB
   A  67  PHE  CG
   A  67  PHE  CD1
   A  67  PHE  CD2
   A  67  PHE  CE1
   A  67  PHE  CE2
   A  67  PHE  CZ            0.051       0.083       46.10   4.1*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.042       0.082       35.00   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.075
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  95  ASP  HA , Angle C-CA-HA, observed: 95.674, delta from target: 13.326
   A  78  ILE  HB , Angle CG2-CB-HB, observed: 94.274, delta from target: 14.726
   A  93  LEU  HA , Angle N-CA-HA, observed: 94.830, delta from target: 15.170
   A  84  GLU  HA , Angle C-CA-HA, observed: 92.541, delta from target: 16.459
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.330, delta from target: 16.670
   A  83  THR  HA , Angle N-CA-HA, observed: 93.031, delta from target: 16.969
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.549, delta from target: 17.451
   A  93  LEU  HA , Angle CB-CA-HA, observed: 127.254, delta from target: -18.254
   A  77  ILE  HA , Angle C-CA-HA, observed: 87.750, delta from target: 21.250
   A  92  THR  HA , Angle N-CA-HA, observed: 88.586, delta from target: 21.414
   A  78  ILE  HA , Angle C-CA-HA, observed: 86.972, delta from target: 22.028
   A  77  ILE  HA , Angle CB-CA-HA, observed: 85.290, delta from target: 23.710
   A  78  ILE  HB , Angle CG1-CB-HB, observed: 141.154, delta from target: -32.154
   A  78  ILE  HB , Angle CA-CB-HB, observed: 60.656, delta from target: 48.344

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.165   2242  Z= 0.658
    Angle     :  2.694  48.344   4079  Z= 1.147
    Chirality :  1.156   5.029    176
    Planarity :  0.011   0.070    327
    Dihedral  : 15.432 108.895    769
    Min Nonbonded Distance : 1.515
  
  Molprobity Statistics.
    All-atom Clashscore : 14.88
    Ramachandran Plot:
      Outliers :  5.11 %
      Allowed  : 10.22 %
      Favored  : 84.67 %
    Rotamer:
      Outliers :  9.68 %
      Allowed  :  4.03 %
      Favored  : 86.29 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 9.92 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.04 (0.66), residues: 137
    helix: -1.34 (0.56), residues: 65
    sheet:  None (None), residues: 0
    loop : -2.75 (0.73), residues: 72
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A 135 
   PHE   0.121   0.016   PHE A  67 
   TYR   0.175   0.027   TYR A  89 
   ARG   0.023   0.006   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A 135 
   PHE   0.083   0.017   PHE A  67 
   TYR   0.141   0.033   TYR A  89 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 0.96, per 1000 atoms: 0.43
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (38.887, 64.596, 67.966, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   5.84 %
                favored =  82.48 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =    14
  Clashscore            =  17.14
  RMS(bonds)            =   0.0103
  RMS(angles)           =   2.34
  MolProbity score      =   2.96

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   5.11 %
                favored =  84.67 %
  Rotamer outliers      =   9.68 %
  C-beta deviations     =    16
  Clashscore            =  14.88
  RMS(bonds)            =   0.0125
  RMS(angles)           =   2.69
  MolProbity score      =   3.09

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   70": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.672)
  Mean delta:    0.013 (Z=  0.676)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.79     4.81  1.00e+00  2.31e+01   4.8*sigma
   A 105  TYR  CA
   A 105  TYR  CB
   A 105  TYR  CG        113.90   122.12    -8.22  1.80e+00  2.09e+01   4.6*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.09     4.51  1.00e+00  2.04e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    9.222 (Z=  4.810)
  Mean delta:    1.866 (Z=  1.011)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00  -149.07   -30.93  5.00e+00  3.83e+01   6.2*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   157.14    22.86  5.00e+00  2.09e+01   4.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   158.65    21.35  5.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.001
  Max. delta:   89.243
  Mean delta:   15.645

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.306
  Mean delta:    0.091

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.068       0.128       93.25   6.4*sigma
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.115       0.102      262.70   5.1*sigma

  Min. delta:    0.000
  Max. delta:    0.115
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2242  Z= 0.481
    Angle     :  1.723   9.222   4079  Z= 0.755
    Chirality :  0.091   0.306    176
    Planarity :  0.012   0.104    327
    Dihedral  : 13.316  89.243    769
    Min Nonbonded Distance : 1.598
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  6.57 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  5.65 %
      Favored  : 90.32 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.37 (0.64), residues: 137
    helix: -0.57 (0.57), residues: 56
    sheet:  None (None), residues: 0
    loop : -1.14 (0.67), residues: 81
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A 139 
   PHE   0.050   0.011   PHE A  67 
   TYR   0.258   0.036   TYR A 105 
   ARG   0.017   0.005   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A 139 
   PHE   0.027   0.008   PHE A  67 
   TYR   0.218   0.041   TYR A 105 
   ARG   0.010   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  93.43 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     1
  Clashscore            =   4.06
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.72
  MolProbity score      =   2.08

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.56    -0.11  1.90e-02  3.14e+01   5.6*sigma
   A 125  LYS  CA
   A 125  LYS  CB          1.53     1.63    -0.10  2.00e-02  2.45e+01   4.9*sigma
   A  89  TYR  N
   A  89  TYR  CA          1.46     1.54    -0.08  1.90e-02  1.96e+01   4.4*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.110 (Z=  5.601)
  Mean delta:    0.017 (Z=  0.855)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   142.93   -21.23  1.80e+00  1.39e+02  11.8*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   137.52   -26.22  2.30e+00  1.30e+02  11.4*sigma
   A 125  LYS  C
   A 125  LYS  CA
   A 125  LYS  CB        110.10    88.50    21.60  1.90e+00  1.29e+02  11.4*sigma
   A  79  LYS  CG
   A  79  LYS  CD
   A  79  LYS  CE        111.30   137.31   -26.01  2.30e+00  1.28e+02  11.3*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   132.84   -21.44  1.90e+00  1.27e+02  11.3*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  CB        110.50   127.38   -16.88  1.70e+00  9.86e+01   9.9*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   106.30    15.40  1.80e+00  7.32e+01   8.6*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20    99.59    16.61  2.00e+00  6.90e+01   8.3*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    94.56    15.54  1.90e+00  6.69e+01   8.2*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   136.34   -14.64  1.80e+00  6.61e+01   8.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    96.79    13.71  1.70e+00  6.50e+01   8.1*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00   131.34   -20.34  2.80e+00  5.28e+01   7.3*sigma
   A 100  GLN  C
   A 101  LYS  N
   A 101  LYS  CA        121.70   134.59   -12.89  1.80e+00  5.13e+01   7.2*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   134.02   -12.32  1.80e+00  4.69e+01   6.8*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   102.69    13.51  2.00e+00  4.56e+01   6.8*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   133.45   -11.75  1.80e+00  4.26e+01   6.5*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    92.92    18.08  2.80e+00  4.17e+01   6.5*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  C         111.00    94.02    16.98  2.80e+00  3.68e+01   6.1*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   123.66   -12.06  2.00e+00  3.64e+01   6.0*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   120.61   -10.21  1.70e+00  3.61e+01   6.0*sigma
   A  93  LEU  CA
   A  93  LEU  CB
   A  93  LEU  CG        116.30   136.42   -20.12  3.50e+00  3.30e+01   5.7*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   125.52    -8.62  1.50e+00  3.30e+01   5.7*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   121.00   -10.90  1.90e+00  3.29e+01   5.7*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   120.90   -10.80  1.90e+00  3.23e+01   5.7*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD2       110.70   127.03   -16.33  3.00e+00  2.96e+01   5.4*sigma
   A 125  LYS  O
   A 125  LYS  C
   A 126  VAL  N         123.00   131.64    -8.64  1.60e+00  2.92e+01   5.4*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   131.18    -9.48  1.80e+00  2.77e+01   5.3*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   119.25    -8.85  1.70e+00  2.71e+01   5.2*sigma
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   118.83    -5.03  1.00e+00  2.53e+01   5.0*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O         120.80   129.26    -8.46  1.70e+00  2.48e+01   5.0*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   106.30     9.90  2.00e+00  2.45e+01   4.9*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   100.93     9.17  1.90e+00  2.33e+01   4.8*sigma
   A 139  HIS  CA
   A 139  HIS  CB
   A 139  HIS  CG        113.80   118.60    -4.80  1.00e+00  2.31e+01   4.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.39    -4.79  1.00e+00  2.30e+01   4.8*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   105.37     6.63  1.40e+00  2.24e+01   4.7*sigma
   A 128  MET  CA
   A 128  MET  CB
   A 128  MET  CG        114.10   104.68     9.42  2.00e+00  2.22e+01   4.7*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   107.14     9.06  2.00e+00  2.05e+01   4.5*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   113.60     8.10  1.80e+00  2.03e+01   4.5*sigma
   A  51  ILE  N
   A  51  ILE  CA
   A  51  ILE  C         111.00   123.55   -12.55  2.80e+00  2.01e+01   4.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.51     5.69  1.30e+00  1.92e+01   4.4*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   128.14    -7.34  1.70e+00  1.87e+01   4.3*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   116.95    -6.45  1.50e+00  1.85e+01   4.3*sigma
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        121.70   129.31    -7.61  1.80e+00  1.79e+01   4.2*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   121.49    -7.59  1.80e+00  1.78e+01   4.2*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   129.20    -7.50  1.80e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50   104.58     6.92  1.70e+00  1.66e+01   4.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   124.28    -8.08  2.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   26.216 (Z= 11.796)
  Mean delta:    3.243 (Z=  1.670)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   -65.53  -114.47  5.00e+00  5.24e+02  22.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   -65.69  -114.31  5.00e+00  5.23e+02  22.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   -72.68  -107.32  5.00e+00  4.61e+02  21.5*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   -96.53   -83.47  5.00e+00  2.79e+02  16.7*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   107.82    72.18  5.00e+00  2.08e+02  14.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -118.09   -61.91  5.00e+00  1.53e+02  12.4*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -118.59   -61.41  5.00e+00  1.51e+02  12.3*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   125.22    54.78  5.00e+00  1.20e+02  11.0*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00  -125.90   -54.10  5.00e+00  1.17e+02  10.8*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -126.46   -53.54  5.00e+00  1.15e+02  10.7*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   129.29    50.71  5.00e+00  1.03e+02  10.1*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   132.35    47.65  5.00e+00  9.08e+01   9.5*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   133.04    46.96  5.00e+00  8.82e+01   9.4*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00  -139.14   -40.86  5.00e+00  6.68e+01   8.2*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   141.73    38.27  5.00e+00  5.86e+01   7.7*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   145.27    34.73  5.00e+00  4.83e+01   6.9*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   145.42    34.58  5.00e+00  4.78e+01   6.9*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   145.89    34.11  5.00e+00  4.66e+01   6.8*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   146.08    33.92  5.00e+00  4.60e+01   6.8*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   147.34    32.66  5.00e+00  4.27e+01   6.5*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   151.27    28.73  5.00e+00  3.30e+01   5.7*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   152.71    27.29  5.00e+00  2.98e+01   5.5*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00  -153.23   -26.77  5.00e+00  2.87e+01   5.4*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -154.70   -25.30  5.00e+00  2.56e+01   5.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   154.98    25.02  5.00e+00  2.50e+01   5.0*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   157.43    22.57  5.00e+00  2.04e+01   4.5*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   157.45    22.55  5.00e+00  2.03e+01   4.5*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   158.25    21.75  5.00e+00  1.89e+01   4.3*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -158.31   -21.69  5.00e+00  1.88e+01   4.3*sigma
   A  38  ILE  CA
   A  38  ILE  C
   A  39  LEU  N
   A  39  LEU  CA        180.00   158.87    21.13  5.00e+00  1.79e+01   4.2*sigma
   A  50  TYR  CA
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        180.00  -158.94   -21.06  5.00e+00  1.77e+01   4.2*sigma
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00  -159.64   -20.36  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.025
  Max. delta:  114.473
  Mean delta:   20.629

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.10     5.61  2.00e-01  7.87e+02  28.0*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.85     5.36  2.00e-01  7.18e+02  26.8*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.57     5.21  2.00e-01  6.79e+02  26.1*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.65     5.18  2.00e-01  6.71e+02  25.9*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  C
   A  52  PRO  CB          2.72    -2.36     5.08  2.00e-01  6.45e+02  25.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.52     5.07  2.00e-01  6.42e+02  25.3*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.52     5.03  2.00e-01  6.34e+02  25.2*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.50     5.01  2.00e-01  6.28e+02  25.1*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -2.46     4.97  2.00e-01  6.17e+02  24.8*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.25     4.69  2.00e-01  5.50e+02  23.5*sigma
   A 130  SER  CA
   A 130  SER  N
   A 130  SER  C
   A 130  SER  CB          2.51    -2.10     4.61  2.00e-01  5.32e+02  23.1*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -2.11     4.54  2.00e-01  5.15e+02  22.7*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -1.85     4.36  2.00e-01  4.76e+02  21.8*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -1.85     4.36  2.00e-01  4.75e+02  21.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.41     3.85  2.00e-01  3.70e+02  19.2*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -1.30     3.81  2.00e-01  3.64e+02  19.1*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51     1.66     0.85  2.00e-01  1.79e+01   4.2*sigma

  Min. delta:    0.000
  Max. delta:    5.609
  Mean delta:    1.461

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.064       0.115       82.63   5.8*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  93  LEU  O
   A  94  GLY  N             0.053       0.091       27.76   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.132
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 127  ARG  HA , Angle CB-CA-HA, observed: 95.732, delta from target: 13.268
   A 127  ARG  HA , Angle C-CA-HA, observed: 95.516, delta from target: 13.484
   A  51  ILE  HA , Angle N-CA-HA, observed: 95.291, delta from target: 14.709
   A  93  LEU  HG , Angle CB-CG-HG, observed: 93.797, delta from target: 15.203
   A 128  MET  HA , Angle C-CA-HA, observed: 93.891, delta from target: 16.109
   A 125  LYS  HA , Angle CB-CA-HA, observed: 125.657, delta from target: -16.657
   A  78  ILE  HA , Angle CB-CA-HA, observed: 89.924, delta from target: 19.076
   A 126  VAL  HA , Angle N-CA-HA, observed: 130.367, delta from target: -20.367
   A  79  LYS  HA , Angle CB-CA-HA, observed: 129.560, delta from target: -20.560
   A 126  VAL  HA , Angle CB-CA-HA, observed: 86.699, delta from target: 22.301
   A 125  LYS  HA , Angle N-CA-HA, observed: 68.155, delta from target: 41.845

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.110   2242  Z= 0.609
    Angle     :  2.808  41.845   4079  Z= 1.220
    Chirality :  1.461   5.609    176
    Planarity :  0.013   0.132    327
    Dihedral  : 16.393 114.473    769
    Min Nonbonded Distance : 1.414
  
  Molprobity Statistics.
    All-atom Clashscore : 26.15
    Ramachandran Plot:
      Outliers : 11.68 %
      Allowed  : 10.22 %
      Favored  : 78.10 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  : 10.48 %
      Favored  : 83.87 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 14.50 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.24 (0.64), residues: 137
    helix: -2.39 (0.50), residues: 63
    sheet:  None (None), residues: 0
    loop : -3.31 (0.74), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 135 
   PHE   0.055   0.016   PHE A  67 
   TYR   0.140   0.014   TYR A  12 
   ARG   0.027   0.004   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 135 
   PHE   0.039   0.016   PHE A  67 
   TYR   0.115   0.015   TYR A  12 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =  11.68 %
                favored =  78.10 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =    16
  Clashscore            =  26.15
  RMS(bonds)            =   0.0118
  RMS(angles)           =   2.81
  MolProbity score      =   3.24

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.57    -0.11  1.90e-02  3.46e+01   5.9*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.63    -0.11  2.10e-02  2.72e+01   5.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.112 (Z=  5.884)
  Mean delta:    0.016 (Z=  0.821)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   131.80   -21.30  1.70e+00  1.57e+02  12.5*sigma
   A  15  PHE  CA
   A  15  PHE  CB
   A  15  PHE  CG        113.80   104.46     9.34  1.00e+00  8.73e+01   9.3*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   123.05   -12.55  1.50e+00  7.01e+01   8.4*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   136.23   -14.53  1.80e+00  6.52e+01   8.1*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   125.27   -15.17  1.90e+00  6.37e+01   8.0*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   135.71   -14.01  1.80e+00  6.06e+01   7.8*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   127.04   -15.44  2.00e+00  5.96e+01   7.7*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    96.37    13.73  1.90e+00  5.22e+01   7.2*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   126.01   -14.41  2.00e+00  5.19e+01   7.2*sigma
   A 124  ALA  O
   A 124  ALA  C
   A 125  LYS  N         123.00   112.44    10.56  1.60e+00  4.35e+01   6.6*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG1       110.40   121.60   -11.20  1.70e+00  4.34e+01   6.6*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   127.22   -13.12  2.00e+00  4.30e+01   6.6*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   133.21   -11.51  1.80e+00  4.09e+01   6.4*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   120.66   -10.16  1.70e+00  3.57e+01   6.0*sigma
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG1       110.40   120.51   -10.11  1.70e+00  3.54e+01   5.9*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   123.31   -11.71  2.00e+00  3.43e+01   5.9*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    95.13    15.87  2.80e+00  3.21e+01   5.7*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   125.27    -8.37  1.50e+00  3.11e+01   5.6*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  78  ILE  O         120.80   111.48     9.32  1.70e+00  3.00e+01   5.5*sigma
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   131.43    -9.73  1.80e+00  2.92e+01   5.4*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   131.12    -9.42  1.80e+00  2.74e+01   5.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   126.57   -10.37  2.00e+00  2.69e+01   5.2*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   119.14    -8.64  1.70e+00  2.58e+01   5.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N         116.20   126.18    -9.98  2.00e+00  2.49e+01   5.0*sigma
   A  86  ILE  N
   A  86  ILE  CA
   A  86  ILE  CB        111.50   119.62    -8.12  1.70e+00  2.28e+01   4.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.23    -4.63  1.00e+00  2.15e+01   4.6*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   129.75    -8.05  1.80e+00  2.00e+01   4.5*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   123.19   -12.19  2.80e+00  1.89e+01   4.4*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   129.53    -7.83  1.80e+00  1.89e+01   4.4*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10   101.91     8.19  1.90e+00  1.86e+01   4.3*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   116.90    -4.30  1.00e+00  1.85e+01   4.3*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   118.22    -8.12  1.90e+00  1.83e+01   4.3*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N         116.20   107.69     8.51  2.00e+00  1.81e+01   4.3*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  CD2       131.20   125.73     5.47  1.30e+00  1.77e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   114.30     7.40  1.80e+00  1.69e+01   4.1*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   129.06    -7.36  1.80e+00  1.67e+01   4.1*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  CB        110.50   117.35    -6.85  1.70e+00  1.62e+01   4.0*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   117.72    -7.62  1.90e+00  1.61e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   21.304 (Z= 12.532)
  Mean delta:    2.831 (Z=  1.539)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00    56.31   123.69  5.00e+00  6.12e+02  24.7*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    89.59    90.41  5.00e+00  3.27e+02  18.1*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   109.97    70.03  5.00e+00  1.96e+02  14.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   114.91    65.09  5.00e+00  1.69e+02  13.0*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -122.56   -57.44  5.00e+00  1.32e+02  11.5*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   126.21    53.79  5.00e+00  1.16e+02  10.8*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   131.78    48.22  5.00e+00  9.30e+01   9.6*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   133.20    46.80  5.00e+00  8.76e+01   9.4*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   134.67    45.33  5.00e+00  8.22e+01   9.1*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA          0.00    44.69   -44.69  5.00e+00  7.99e+01   8.9*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -135.98   -44.02  5.00e+00  7.75e+01   8.8*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   139.36    40.64  5.00e+00  6.61e+01   8.1*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   140.51    39.49  5.00e+00  6.24e+01   7.9*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA          0.00    37.45   -37.45  5.00e+00  5.61e+01   7.5*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   144.57    35.43  5.00e+00  5.02e+01   7.1*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -145.85   -34.15  5.00e+00  4.67e+01   6.8*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   145.88    34.12  5.00e+00  4.66e+01   6.8*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00  -148.26   -31.74  5.00e+00  4.03e+01   6.3*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   149.11    30.89  5.00e+00  3.82e+01   6.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -151.10   -28.90  5.00e+00  3.34e+01   5.8*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   152.30    27.70  5.00e+00  3.07e+01   5.5*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   152.99    27.01  5.00e+00  2.92e+01   5.4*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -154.86   -25.14  5.00e+00  2.53e+01   5.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -156.72   -23.28  5.00e+00  2.17e+01   4.7*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   157.44    22.56  5.00e+00  2.04e+01   4.5*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   157.64    22.36  5.00e+00  2.00e+01   4.5*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   159.36    20.64  5.00e+00  1.70e+01   4.1*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00  -159.66   -20.34  5.00e+00  1.65e+01   4.1*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   159.87    20.13  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001
  Max. delta:  123.687
  Mean delta:   19.581

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.98     5.50  2.00e-01  7.57e+02  27.5*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.87     5.38  2.00e-01  7.23e+02  26.9*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.75     5.26  2.00e-01  6.91e+02  26.3*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.61     5.25  2.00e-01  6.90e+02  26.3*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.45     5.09  2.00e-01  6.48e+02  25.5*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.35     4.99  2.00e-01  6.23e+02  25.0*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -2.37     4.88  2.00e-01  5.96e+02  24.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.22     4.77  2.00e-01  5.68e+02  23.8*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -2.20     4.71  2.00e-01  5.56e+02  23.6*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.18     4.69  2.00e-01  5.50e+02  23.4*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.24     4.68  2.00e-01  5.47e+02  23.4*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.68     4.11  2.00e-01  4.22e+02  20.5*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.85     3.28  2.00e-01  2.70e+02  16.4*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -0.56     3.07  2.00e-01  2.36e+02  15.4*sigma
   A  14  VAL  CA
   A  14  VAL  N
   A  14  VAL  C
   A  14  VAL  CB          2.44     1.63     0.81  2.00e-01  1.64e+01   4.0*sigma

  Min. delta:    0.001
  Max. delta:    5.501
  Mean delta:    1.351

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.220       0.365      847.04  18.2*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.057       0.108       65.13   5.4*sigma
   A 128  MET  CA
   A 128  MET  C
   A 128  MET  O
   A 129  ARG  N             0.056       0.096       31.01   4.8*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.113       0.095      254.98   4.8*sigma

  Min. delta:    0.000
  Max. delta:    0.220
  Mean delta:    0.025

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    3" pdbres="HIS A  43  conformer  : HE2, HD1 
    3" pdbres="HIS A 134  conformer  : HE2, HD1 
    3" pdbres="HIS A 135  conformer  : HE2, HD1 
    3" pdbres="HIS A 136  conformer  : HE2, HD1 
    3" pdbres="HIS A 137  conformer  : HE2, HD1 
    3" pdbres="HIS A 138  conformer  : HE2, HD1 
    3" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  92  THR  HB , Angle CA-CB-HB, observed: 96.290, delta from target: 12.710
   A  93  LEU  HA , Angle C-CA-HA, observed: 121.940, delta from target: -12.940
   A 127  ARG  HA , Angle C-CA-HA, observed: 95.701, delta from target: 13.299
   A  78  ILE  HA , Angle CB-CA-HA, observed: 95.524, delta from target: 13.476
   A  86  ILE  HA , Angle N-CA-HA, observed: 96.512, delta from target: 13.488
   A  81  TYR  HA , Angle N-CA-HA, observed: 96.074, delta from target: 13.926
   A  78  ILE  HB , Angle CA-CB-HB, observed: 94.196, delta from target: 14.804
   A 124  ALA  HA , Angle CB-CA-HA, observed: 94.087, delta from target: 14.913
   A  78  ILE  HA , Angle C-CA-HA, observed: 90.454, delta from target: 18.546
   A  81  TYR  HA , Angle C-CA-HA, observed: 128.361, delta from target: -19.361
   A  51  ILE  HA , Angle C-CA-HA, observed: 86.871, delta from target: 22.129
   A  89  TYR  HA , Angle C-CA-HA, observed: 84.739, delta from target: 24.261
   A  51  ILE  HA , Angle CB-CA-HA, observed: 84.713, delta from target: 24.287
   A  89  TYR  HA , Angle CB-CA-HA, observed: 79.783, delta from target: 29.217

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.112   2242  Z= 0.585
    Angle     :  2.611  29.217   4079  Z= 1.147
    Chirality :  1.351   5.501    176
    Planarity :  0.019   0.230    327
    Dihedral  : 15.999 123.687    769
    Min Nonbonded Distance : 1.418
  
  Molprobity Statistics.
    All-atom Clashscore : 17.58
    Ramachandran Plot:
      Outliers : 10.95 %
      Allowed  : 13.14 %
      Favored  : 75.91 %
    Rotamer:
      Outliers :  8.06 %
      Allowed  :  8.06 %
      Favored  : 83.87 %
    Cbeta Deviations : 15.15 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 14.50 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.48 (0.58), residues: 137
    helix: -1.77 (0.53), residues: 62
    sheet:  None (None), residues: 0
    loop : -4.28 (0.58), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A 139 
   PHE   0.559   0.070   PHE A  15 
   TYR   0.260   0.034   TYR A  81 
   ARG   0.045   0.011   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A 139 
   PHE   0.365   0.073   PHE A  15 
   TYR   0.208   0.038   TYR A  81 
   ARG   0.003   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.61    -0.15  1.60e-02  9.34e+01   9.7*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.66    -0.13  2.10e-02  4.07e+01   6.4*sigma
   A  89  TYR  C
   A  90  SER  N           1.33     1.40    -0.07  1.40e-02  2.43e+01   4.9*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.27     0.06  1.40e-02  1.71e+01   4.1*sigma
   A  89  TYR  N
   A  89  TYR  CA          1.46     1.53    -0.08  1.90e-02  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.155 (Z=  9.663)
  Mean delta:    0.017 (Z=  0.893)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   140.42   -18.72  1.80e+00  1.08e+02  10.4*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   133.78   -19.68  2.00e+00  9.69e+01   9.8*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   135.82   -19.62  2.00e+00  9.62e+01   9.8*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   127.10   -17.00  1.90e+00  8.01e+01   8.9*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    96.16    14.34  1.70e+00  7.11e+01   8.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   136.48   -14.78  1.80e+00  6.74e+01   8.2*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   124.26   -13.76  1.70e+00  6.55e+01   8.1*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   110.29    12.71  1.60e+00  6.31e+01   7.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.32   -11.42  1.50e+00  5.80e+01   7.6*sigma
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        121.70   134.73   -13.03  1.80e+00  5.24e+01   7.2*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   129.20   -18.20  2.80e+00  4.23e+01   6.5*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   119.04    -6.44  1.00e+00  4.15e+01   6.4*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.80   -11.10  1.80e+00  3.81e+01   6.2*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N         116.20   104.48    11.72  2.00e+00  3.44e+01   5.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.34    -5.74  1.00e+00  3.30e+01   5.7*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   126.97   -10.77  2.00e+00  2.90e+01   5.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.05   -10.45  2.00e+00  2.73e+01   5.2*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   118.96    -8.46  1.70e+00  2.48e+01   5.0*sigma
   A  70  LEU  N
   A  70  LEU  CA
   A  70  LEU  CB        110.50   102.07     8.43  1.70e+00  2.46e+01   5.0*sigma
   A  83  THR  CA
   A  83  THR  CB
   A  83  THR  CG2       110.50   118.82    -8.32  1.70e+00  2.39e+01   4.9*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   115.78     7.22  1.60e+00  2.03e+01   4.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  89  TYR  O         120.80   113.53     7.27  1.70e+00  1.83e+01   4.3*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   103.34     7.16  1.70e+00  1.77e+01   4.2*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.77e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.75e+01   4.2*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   117.56    -7.06  1.70e+00  1.72e+01   4.2*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   117.94    -7.84  1.90e+00  1.70e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O         120.80   113.81     6.99  1.70e+00  1.69e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.87     6.93  1.70e+00  1.66e+01   4.1*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   129.03    -7.33  1.80e+00  1.66e+01   4.1*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  C         111.00   122.26   -11.26  2.80e+00  1.62e+01   4.0*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N         116.20   108.16     8.04  2.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   19.683 (Z= 10.398)
  Mean delta:    2.719 (Z=  1.460)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   -52.01  -127.99  5.00e+00  6.55e+02  25.6*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   122.26    57.74  5.00e+00  1.33e+02  11.5*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -135.23   -44.77  5.00e+00  8.02e+01   9.0*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   136.23    43.77  5.00e+00  7.66e+01   8.8*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00  -139.32   -40.68  5.00e+00  6.62e+01   8.1*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA          0.00   -34.61    34.61  5.00e+00  4.79e+01   6.9*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   145.47    34.53  5.00e+00  4.77e+01   6.9*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   148.84    31.16  5.00e+00  3.88e+01   6.2*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   148.90    31.10  5.00e+00  3.87e+01   6.2*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   150.55    29.45  5.00e+00  3.47e+01   5.9*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   153.60    26.40  5.00e+00  2.79e+01   5.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00  -155.98   -24.02  5.00e+00  2.31e+01   4.8*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   157.56    22.44  5.00e+00  2.01e+01   4.5*sigma

  Min. delta:    0.079
  Max. delta:  127.995
  Mean delta:   16.146

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -2.55     4.98  2.00e-01  6.20e+02  24.9*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.30     4.94  2.00e-01  6.10e+02  24.7*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.04     4.55  2.00e-01  5.18e+02  22.7*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -1.85     4.36  2.00e-01  4.76e+02  21.8*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.07     3.51  2.00e-01  3.07e+02  17.5*sigma
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51     0.72     1.79  2.00e-01  8.04e+01   9.0*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43     1.34     1.09  2.00e-01  2.98e+01   5.5*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51     1.44     1.07  2.00e-01  2.86e+01   5.4*sigma

  Min. delta:    0.001
  Max. delta:    4.981
  Mean delta:    0.791

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.085
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  90  SER  HA , Angle CB-CA-HA, observed: 96.686, delta from target: 12.314
   A  78  ILE  HA , Angle C-CA-HA, observed: 96.016, delta from target: 12.984
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.204, delta from target: 15.796
   A  74  ASP  HA , Angle C-CA-HA, observed: 92.428, delta from target: 16.572
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.012, delta from target: 16.988
   A  91  TYR  HA , Angle C-CA-HA, observed: 91.847, delta from target: 17.153
   A  99  LEU  HA , Angle CB-CA-HA, observed: 86.863, delta from target: 22.137
   A  78  ILE  HA , Angle N-CA-HA, observed: 82.591, delta from target: 27.409
   A  99  LEU  HA , Angle C-CA-HA, observed: 78.713, delta from target: 30.287

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.155   2242  Z= 0.636
    Angle     :  2.478  30.287   4079  Z= 1.085
    Chirality :  0.791   4.981    176
    Planarity :  0.011   0.085    327
    Dihedral  : 13.482 127.995    769
    Min Nonbonded Distance : 1.461
  
  Molprobity Statistics.
    All-atom Clashscore : 10.82
    Ramachandran Plot:
      Outliers : 10.22 %
      Allowed  :  7.30 %
      Favored  : 82.48 %
    Rotamer:
      Outliers :  8.87 %
      Allowed  :  4.03 %
      Favored  : 87.10 %
    Cbeta Deviations :  8.33 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 6.87 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.63 (0.67), residues: 137
    helix: -1.33 (0.52), residues: 68
    sheet:  None (None), residues: 0
    loop : -2.18 (0.80), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A  43 
   PHE   0.050   0.014   PHE A  15 
   TYR   0.120   0.019   TYR A  50 
   ARG   0.034   0.006   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A  43 
   PHE   0.034   0.012   PHE A  15 
   TYR   0.096   0.023   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.055 (Z=  2.795)
  Mean delta:    0.014 (Z=  0.710)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50    96.81    13.69  1.70e+00  6.48e+01   8.1*sigma
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        121.70   135.49   -13.79  1.80e+00  5.87e+01   7.7*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   124.62   -14.52  1.90e+00  5.84e+01   7.6*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.00   -11.10  1.50e+00  5.48e+01   7.4*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   134.59   -12.89  1.80e+00  5.13e+01   7.2*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.87   -10.17  1.80e+00  3.19e+01   5.6*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.24    -5.64  1.00e+00  3.18e+01   5.6*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N         116.20   127.08   -10.88  2.00e+00  2.96e+01   5.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.84   -10.24  2.00e+00  2.62e+01   5.1*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  C         111.00   124.65   -13.65  2.80e+00  2.38e+01   4.9*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   119.08    -8.98  1.90e+00  2.24e+01   4.7*sigma
   A 138  HIS  O
   A 138  HIS  C
   A 139  HIS  N         123.00   115.98     7.02  1.60e+00  1.93e+01   4.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   107.66     8.54  2.00e+00  1.82e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   129.16    -7.46  1.80e+00  1.72e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00   122.26   -11.26  2.80e+00  1.62e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:   14.520 (Z=  8.053)
  Mean delta:    2.322 (Z=  1.262)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   110.31    69.69  5.00e+00  1.94e+02  13.9*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   121.75    58.25  5.00e+00  1.36e+02  11.6*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   124.44    55.56  5.00e+00  1.23e+02  11.1*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -131.19   -48.81  5.00e+00  9.53e+01   9.8*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -142.56   -37.44  5.00e+00  5.61e+01   7.5*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   143.96    36.04  5.00e+00  5.20e+01   7.2*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00  -147.81   -32.19  5.00e+00  4.15e+01   6.4*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   148.16    31.84  5.00e+00  4.06e+01   6.4*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   156.98    23.02  5.00e+00  2.12e+01   4.6*sigma

  Min. delta:    0.053
  Max. delta:   73.181
  Mean delta:   15.245

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.50     5.01  2.00e-01  6.27e+02  25.0*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.30     4.81  2.00e-01  5.80e+02  24.1*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.06     3.49  2.00e-01  3.05e+02  17.5*sigma

  Min. delta:    0.001
  Max. delta:    5.010
  Mean delta:    0.601

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.052
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  92  THR  HA , Angle N-CA-HA, observed: 97.947, delta from target: 12.053
   A  93  LEU  HA , Angle CB-CA-HA, observed: 123.386, delta from target: -14.386
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.257, delta from target: 15.743
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.236, delta from target: 16.764
   A  74  ASP  HA , Angle N-CA-HA, observed: 127.149, delta from target: -17.149

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.055   2242  Z= 0.506
    Angle     :  2.103  17.149   4079  Z= 0.931
    Chirality :  0.601   5.010    176
    Planarity :  0.009   0.048    327
    Dihedral  : 12.913  73.181    769
    Min Nonbonded Distance : 1.477
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  : 11.68 %
      Favored  : 85.40 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  3.23 %
      Favored  : 91.13 %
    Cbeta Deviations :  6.06 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 6.11 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.50 (0.64), residues: 137
    helix: -1.27 (0.47), residues: 79
    sheet:  None (None), residues: 0
    loop : -2.11 (0.85), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.012   0.004   PHE A  45 
   TYR   0.119   0.017   TYR A 111 
   ARG   0.028   0.007   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.007   0.004   PHE A  15 
   TYR   0.098   0.020   TYR A 111 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =  10.95 %
                favored =  75.91 %
  Rotamer outliers      =   8.06 %
  C-beta deviations     =    20
  Clashscore            =  17.58
  RMS(bonds)            =   0.0113
  RMS(angles)           =   2.61
  MolProbity score      =   3.22

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =  10.22 %
                favored =  82.48 %
  Rotamer outliers      =   8.87 %
  C-beta deviations     =    11
  Clashscore            =  10.82
  RMS(bonds)            =   0.0119
  RMS(angles)           =   2.48
  MolProbity score      =   2.97

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.713, 52.459, 75.397, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   2.92 %
                favored =  85.40 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     8
  Clashscore            =   3.16
  RMS(bonds)            =   0.0098
  RMS(angles)           =   2.10
  MolProbity score      =   2.33

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 130}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.65    -0.20  1.60e-02  1.56e+02  12.5*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.69    -0.17  2.10e-02  6.21e+01   7.9*sigma
   A  90  SER  N
   A  90  SER  CA          1.46     1.58    -0.13  1.90e-02  4.38e+01   6.6*sigma
   A  93  LEU  C
   A  94  GLY  N           1.33     1.27     0.06  1.40e-02  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.200 (Z= 12.505)
  Mean delta:    0.017 (Z=  0.923)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   142.92   -21.22  1.80e+00  1.39e+02  11.8*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   137.18   -26.18  2.80e+00  8.74e+01   9.3*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   124.73   -14.23  1.70e+00  7.01e+01   8.4*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   123.72   -13.22  1.70e+00  6.05e+01   7.8*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.79   -10.89  1.50e+00  5.27e+01   7.3*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10   123.06   -12.96  1.90e+00  4.66e+01   6.8*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   103.10    13.10  2.00e+00  4.29e+01   6.5*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   121.34   -10.84  1.70e+00  4.07e+01   6.4*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10    99.15    10.95  1.90e+00  3.32e+01   5.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.90   -11.30  2.00e+00  3.19e+01   5.6*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   120.00    -9.60  1.70e+00  3.19e+01   5.6*sigma
   A  98  SER  C
   A  98  SER  CA
   A  98  SER  CB        110.10    99.50    10.60  1.90e+00  3.11e+01   5.6*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.17    -5.57  1.00e+00  3.11e+01   5.6*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    99.72    10.38  1.90e+00  2.99e+01   5.5*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   101.46     9.04  1.70e+00  2.83e+01   5.3*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   123.46    -9.56  1.80e+00  2.82e+01   5.3*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.88    -5.28  1.00e+00  2.79e+01   5.3*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   119.36    -8.86  1.70e+00  2.71e+01   5.2*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   101.24    10.36  2.00e+00  2.68e+01   5.2*sigma
   A  97  SER  O
   A  97  SER  C
   A  98  SER  N         123.00   131.18    -8.18  1.60e+00  2.61e+01   5.1*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   130.77    -9.07  1.80e+00  2.54e+01   5.0*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N         116.20   106.17    10.03  2.00e+00  2.52e+01   5.0*sigma
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        121.70   130.63    -8.93  1.80e+00  2.46e+01   5.0*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   123.87    -9.77  2.00e+00  2.39e+01   4.9*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   115.25     7.75  1.60e+00  2.35e+01   4.8*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   119.08    -8.98  1.90e+00  2.23e+01   4.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   130.00    -8.30  1.80e+00  2.12e+01   4.6*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   102.68     7.82  1.70e+00  2.12e+01   4.6*sigma
   A  78  ILE  CB
   A  78  ILE  CG1
   A  78  ILE  CD1       113.80   123.34    -9.54  2.10e+00  2.06e+01   4.5*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   129.79    -8.09  1.80e+00  2.02e+01   4.5*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   104.02     7.48  1.70e+00  1.94e+01   4.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   107.61     8.59  2.00e+00  1.84e+01   4.3*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N         116.20   107.63     8.57  2.00e+00  1.84e+01   4.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   129.40    -7.70  1.80e+00  1.83e+01   4.3*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   116.17     6.83  1.60e+00  1.82e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.35     4.25  1.00e+00  1.81e+01   4.3*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.72     5.48  1.30e+00  1.77e+01   4.2*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.26    -5.86  1.40e+00  1.75e+01   4.2*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   121.29    -7.39  1.80e+00  1.69e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.88     5.32  1.30e+00  1.68e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.92     6.88  1.70e+00  1.64e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   26.180 (Z= 11.786)
  Mean delta:    2.752 (Z=  1.475)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   -65.71  -114.29  5.00e+00  5.22e+02  22.9*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -68.49  -111.51  5.00e+00  4.97e+02  22.3*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   -96.03   -83.97  5.00e+00  2.82e+02  16.8*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00  -106.02   -73.98  5.00e+00  2.19e+02  14.8*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -114.25   -65.75  5.00e+00  1.73e+02  13.2*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -117.34   -62.66  5.00e+00  1.57e+02  12.5*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   124.27    55.73  5.00e+00  1.24e+02  11.1*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   130.92    49.08  5.00e+00  9.63e+01   9.8*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   135.88    44.12  5.00e+00  7.79e+01   8.8*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -136.79   -43.21  5.00e+00  7.47e+01   8.6*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA          0.00   -38.40    38.40  5.00e+00  5.90e+01   7.7*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   145.16    34.84  5.00e+00  4.86e+01   7.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   145.80    34.20  5.00e+00  4.68e+01   6.8*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   146.88    33.12  5.00e+00  4.39e+01   6.6*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00  -147.26   -32.74  5.00e+00  4.29e+01   6.5*sigma
   A 100  GLN  CA
   A 100  GLN  C
   A 101  LYS  N
   A 101  LYS  CA        180.00  -147.82   -32.18  5.00e+00  4.14e+01   6.4*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   148.54    31.46  5.00e+00  3.96e+01   6.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   151.34    28.66  5.00e+00  3.28e+01   5.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -152.36   -27.64  5.00e+00  3.06e+01   5.5*sigma
   A  71  ILE  CA
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        180.00  -153.84   -26.16  5.00e+00  2.74e+01   5.2*sigma
   A 101  LYS  CA
   A 101  LYS  C
   A 102  PRO  N
   A 102  PRO  CA        180.00  -155.12   -24.88  5.00e+00  2.48e+01   5.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   155.23    24.77  5.00e+00  2.45e+01   5.0*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -156.24   -23.76  5.00e+00  2.26e+01   4.8*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   156.43    23.57  5.00e+00  2.22e+01   4.7*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   156.98    23.02  5.00e+00  2.12e+01   4.6*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   157.40    22.60  5.00e+00  2.04e+01   4.5*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   159.91    20.09  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.010
  Max. delta:  114.289
  Mean delta:   19.357

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.70     5.23  2.00e-01  6.83e+02  26.1*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.61     5.12  2.00e-01  6.57e+02  25.6*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.40     5.05  2.00e-01  6.36e+02  25.2*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.17     4.68  2.00e-01  5.47e+02  23.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -1.91     4.46  2.00e-01  4.98e+02  22.3*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.22     3.66  2.00e-01  3.34e+02  18.3*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -0.84     3.35  2.00e-01  2.81e+02  16.8*sigma
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51     1.58     0.93  2.00e-01  2.16e+01   4.6*sigma

  Min. delta:    0.000
  Max. delta:    5.227
  Mean delta:    0.923

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  67  PHE  CB
   A  67  PHE  CG
   A  67  PHE  CD1
   A  67  PHE  CD2
   A  67  PHE  CE1
   A  67  PHE  CE2
   A  67  PHE  CZ            0.117       0.191      240.09   9.5*sigma
   A  98  SER  CA
   A  98  SER  C
   A  98  SER  O
   A  99  LEU  N             0.090       0.155       80.20   7.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  78  ILE  O
   A  79  LYS  N             0.084       0.146       70.98   7.3*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.070       0.125       97.92   6.2*sigma

  Min. delta:    0.000
  Max. delta:    0.117
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  92  THR  HB , Angle CA-CB-HB, observed: 96.507, delta from target: 12.493
   A  91  TYR  HA , Angle C-CA-HA, observed: 121.736, delta from target: -12.736
   A  51  ILE  HA , Angle CB-CA-HA, observed: 94.103, delta from target: 14.897
   A  88  ASP  HA , Angle N-CA-HA, observed: 94.908, delta from target: 15.092
   A  90  SER  HA , Angle C-CA-HA, observed: 124.254, delta from target: -15.254
   A  89  TYR  HA , Angle C-CA-HA, observed: 93.243, delta from target: 15.757
   A  78  ILE  HB , Angle CG1-CB-HB, observed: 93.181, delta from target: 15.819
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.615, delta from target: 17.385
   A  89  TYR  HA , Angle CB-CA-HA, observed: 140.546, delta from target: -31.546
   A  89  TYR  HA , Angle N-CA-HA, observed: 65.410, delta from target: 44.590

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.200   2242  Z= 0.657
    Angle     :  2.531  44.590   4079  Z= 1.102
    Chirality :  0.923   5.227    176
    Planarity :  0.015   0.124    327
    Dihedral  : 15.705 114.289    769
    Min Nonbonded Distance : 1.411
  
  Molprobity Statistics.
    All-atom Clashscore : 16.23
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  : 10.22 %
      Favored  : 83.21 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  5.65 %
      Favored  : 87.10 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 12.98 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.33 (0.63), residues: 137
    helix: -2.72 (0.49), residues: 71
    sheet:  None (None), residues: 0
    loop : -3.04 (0.76), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A 136 
   PHE   0.284   0.038   PHE A  67 
   TYR   0.152   0.021   TYR A  12 
   ARG   0.022   0.004   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A 136 
   PHE   0.191   0.042   PHE A  67 
   TYR   0.125   0.024   TYR A  12 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 135  HIS
   A 136  HIS

=================================== Summary ===================================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.039 (Z=  3.285)
  Mean delta:    0.013 (Z=  0.677)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   131.37    -9.67  1.80e+00  2.88e+01   5.4*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.16     4.44  1.00e+00  1.97e+01   4.4*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:   11.062 (Z=  5.370)
  Mean delta:    1.948 (Z=  1.062)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   158.68    21.32  5.00e+00  1.82e+01   4.3*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   159.53    20.47  5.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.062
  Max. delta:   72.409
  Mean delta:   13.087

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.355
  Mean delta:    0.098

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.124       0.123      308.11   6.1*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.061       0.110       74.88   5.5*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  ND1
   A 137  HIS  CD2
   A 137  HIS  CE1
   A 137  HIS  NE2           0.073       0.098       81.03   4.9*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.049       0.094       47.72   4.7*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  85  LYS  O
   A  86  ILE  N             0.047       0.082       22.24   4.1*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.044       0.081       39.41   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.124
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.482
    Angle     :  1.787  11.062   4079  Z= 0.788
    Chirality :  0.098   0.355    176
    Planarity :  0.015   0.121    327
    Dihedral  : 11.095  72.409    769
    Min Nonbonded Distance : 1.621
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  5.11 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  3.23 %
      Favored  : 95.97 %
    Cbeta Deviations :  1.52 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.81 (0.69), residues: 137
    helix: -1.13 (0.51), residues: 63
    sheet:  None (None), residues: 0
    loop :  0.21 (0.81), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A 137 
   PHE   0.077   0.017   PHE A  67 
   TYR   0.320   0.036   TYR A  89 
   ARG   0.072   0.016   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A 137 
   PHE   0.049   0.015   PHE A  67 
   TYR   0.244   0.043   TYR A  89 
   ARG   0.004   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 0.75, per 1000 atoms: 0.34
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.869, 39.586, 55.638, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   6.57 %
                favored =  83.21 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    14
  Clashscore            =  16.23
  RMS(bonds)            =   0.0124
  RMS(angles)           =   2.53
  MolProbity score      =   3.06

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.56    -0.11  1.60e-02  4.66e+01   6.8*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.59    -0.13  1.90e-02  4.64e+01   6.8*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.64    -0.12  2.10e-02  3.16e+01   5.6*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.129 (Z=  6.829)
  Mean delta:    0.016 (Z=  0.848)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   133.32   -21.72  2.00e+00  1.18e+02  10.9*sigma
   A 129  ARG  CB
   A 129  ARG  CG
   A 129  ARG  CD        111.30   134.52   -23.22  2.30e+00  1.02e+02  10.1*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   139.55   -17.85  1.80e+00  9.83e+01   9.9*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   105.56    16.14  1.80e+00  8.04e+01   9.0*sigma
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        121.70   136.74   -15.04  1.80e+00  6.99e+01   8.4*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   125.90   -15.80  1.90e+00  6.92e+01   8.3*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   124.52   -14.02  1.70e+00  6.80e+01   8.2*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   124.71   -14.61  1.90e+00  5.91e+01   7.7*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   123.56   -13.06  1.70e+00  5.90e+01   7.7*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   135.01   -13.31  1.80e+00  5.47e+01   7.4*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   108.59    13.11  1.80e+00  5.30e+01   7.3*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.26   -12.56  1.80e+00  4.87e+01   7.0*sigma
   A  76  SER  N
   A  76  SER  CA
   A  76  SER  CB        110.50    98.76    11.74  1.70e+00  4.77e+01   6.9*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   126.27   -12.17  2.00e+00  3.70e+01   6.1*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   122.16   -13.06  2.20e+00  3.52e+01   5.9*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   124.44   -10.54  1.80e+00  3.43e+01   5.9*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N         116.20   127.67   -11.47  2.00e+00  3.29e+01   5.7*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.02   -10.32  1.80e+00  3.29e+01   5.7*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.01   -10.31  1.80e+00  3.28e+01   5.7*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   111.63    10.07  1.80e+00  3.13e+01   5.6*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   119.85    -9.45  1.70e+00  3.09e+01   5.6*sigma
   A 136  HIS  O
   A 136  HIS  C
   A 137  HIS  N         123.00   114.13     8.87  1.60e+00  3.08e+01   5.5*sigma
   A  52  PRO  C
   A  53  LEU  N
   A  53  LEU  CA        121.70   131.58    -9.88  1.80e+00  3.01e+01   5.5*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   119.82    -9.32  1.70e+00  3.00e+01   5.5*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   120.51   -10.41  1.90e+00  3.00e+01   5.5*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N         116.20   105.36    10.84  2.00e+00  2.94e+01   5.4*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   124.72    -7.82  1.50e+00  2.72e+01   5.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   126.63   -10.43  2.00e+00  2.72e+01   5.2*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.61    -5.01  1.00e+00  2.51e+01   5.0*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   130.02    -8.32  1.80e+00  2.14e+01   4.6*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   107.31     8.89  2.00e+00  1.98e+01   4.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   125.08    -8.88  2.00e+00  1.97e+01   4.4*sigma
   A 119  LEU  C
   A 119  LEU  CA
   A 119  LEU  CB        110.10   118.40    -8.30  1.90e+00  1.91e+01   4.4*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   129.53    -7.83  1.80e+00  1.89e+01   4.3*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   113.92     7.78  1.80e+00  1.87e+01   4.3*sigma
   A  76  SER  CA
   A  76  SER  CB
   A  76  SER  OG        111.10   119.68    -8.58  2.00e+00  1.84e+01   4.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  89  TYR  O         120.80   113.56     7.24  1.70e+00  1.82e+01   4.3*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    99.16    11.84  2.80e+00  1.79e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.75e+01   4.2*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   116.69    -4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.006 (Z=  0.003)
  Max. delta:   23.222 (Z= 10.859)
  Mean delta:    2.904 (Z=  1.558)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   -80.91   -99.09  5.00e+00  3.93e+02  19.8*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00    83.52    96.48  5.00e+00  3.72e+02  19.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00    88.94    91.06  5.00e+00  3.32e+02  18.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -99.66   -80.34  5.00e+00  2.58e+02  16.1*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   116.47    63.53  5.00e+00  1.61e+02  12.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   135.15    44.85  5.00e+00  8.05e+01   9.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -135.23   -44.77  5.00e+00  8.02e+01   9.0*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   138.24    41.76  5.00e+00  6.97e+01   8.4*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -147.02   -32.98  5.00e+00  4.35e+01   6.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA          0.00    30.23   -30.23  5.00e+00  3.66e+01   6.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -149.94   -30.06  5.00e+00  3.61e+01   6.0*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -153.84   -26.16  5.00e+00  2.74e+01   5.2*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -153.98   -26.02  5.00e+00  2.71e+01   5.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   155.51    24.49  5.00e+00  2.40e+01   4.9*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00  -155.71   -24.29  5.00e+00  2.36e+01   4.9*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   157.43    22.57  5.00e+00  2.04e+01   4.5*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   157.57    22.43  5.00e+00  2.01e+01   4.5*sigma

  Min. delta:    0.009
  Max. delta:   99.092
  Mean delta:   18.311

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.85     5.49  2.00e-01  7.55e+02  27.5*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.86     5.37  2.00e-01  7.22e+02  26.9*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  C
   A  52  PRO  CB          2.72    -2.46     5.18  2.00e-01  6.71e+02  25.9*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.45     4.96  2.00e-01  6.14e+02  24.8*sigma
   A 133  GLU  CA
   A 133  GLU  N
   A 133  GLU  C
   A 133  GLU  CB          2.51    -2.32     4.83  2.00e-01  5.84e+02  24.2*sigma
   A   2  LEU  CA
   A   2  LEU  N
   A   2  LEU  C
   A   2  LEU  CB          2.51    -2.15     4.66  2.00e-01  5.44e+02  23.3*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -2.14     4.65  2.00e-01  5.41e+02  23.3*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.00     4.55  2.00e-01  5.18e+02  22.8*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.96     4.47  2.00e-01  5.00e+02  22.4*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.73     4.17  2.00e-01  4.34e+02  20.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.29     3.72  2.00e-01  3.46e+02  18.6*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     0.90     1.61  2.00e-01  6.48e+01   8.1*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51     1.58     0.93  2.00e-01  2.17e+01   4.7*sigma

  Min. delta:    0.001
  Max. delta:    5.495
  Mean delta:    1.209

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.119       0.231      284.86  11.6*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.061       0.118       74.88   5.9*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O
   A  91  TYR  N             0.058       0.101       34.16   5.0*sigma

  Min. delta:    0.000
  Max. delta:    0.155
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  51  ILE  HA , Angle C-CA-HA, observed: 95.990, delta from target: 13.010
   A  89  TYR  HA , Angle CB-CA-HA, observed: 95.285, delta from target: 13.715
   A  79  LYS  HA , Angle C-CA-HA, observed: 123.057, delta from target: -14.057
   A  92  THR  HA , Angle C-CA-HA, observed: 94.877, delta from target: 14.123
   A  90  SER  HA , Angle N-CA-HA, observed: 93.439, delta from target: 16.561
   A  78  ILE  HA , Angle N-CA-HA, observed: 128.777, delta from target: -18.777
   A  78  ILE  HA , Angle CB-CA-HA, observed: 89.027, delta from target: 19.973
   A  97  SER  HA , Angle CB-CA-HA, observed: 87.782, delta from target: 21.218
   A  97  SER  HA , Angle C-CA-HA, observed: 87.324, delta from target: 21.676
   A  78  ILE  HA , Angle C-CA-HA, observed: 82.884, delta from target: 26.116

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.129   2242  Z= 0.604
    Angle     :  2.575  26.116   4079  Z= 1.140
    Chirality :  1.209   5.495    176
    Planarity :  0.015   0.155    327
    Dihedral  : 15.124  99.092    769
    Min Nonbonded Distance : 1.760
  
  Molprobity Statistics.
    All-atom Clashscore : 7.21
    Ramachandran Plot:
      Outliers : 10.95 %
      Allowed  :  7.30 %
      Favored  : 81.75 %
    Rotamer:
      Outliers :  8.87 %
      Allowed  :  5.65 %
      Favored  : 85.48 %
    Cbeta Deviations : 12.88 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 7.63 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.63 (0.56), residues: 137
    helix: -2.29 (0.43), residues: 80
    sheet:  None (None), residues: 0
    loop : -4.25 (0.71), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A  43 
   PHE   0.091   0.015   PHE A  15 
   TYR   0.301   0.028   TYR A  89 
   ARG   0.016   0.003   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A  43 
   PHE   0.060   0.014   PHE A  15 
   TYR   0.231   0.033   TYR A  89 
   ARG   0.002   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.565)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.597 (Z=  1.368)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   80.412
  Mean delta:   23.467

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.094
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.045
    Angle     :  0.980   4.833   4077  Z= 0.342
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.238  80.412    768
    Min Nonbonded Distance : 1.468
  
  Molprobity Statistics.
    All-atom Clashscore : 29.32
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  : 18.25 %
      Favored  : 78.83 %
    Rotamer:
      Outliers : 26.61 %
      Allowed  : 15.32 %
      Favored  : 58.06 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.70 (0.43), residues: 137
    helix: -4.21 (0.33), residues: 65
    sheet:  None (None), residues: 0
    loop : -4.86 (0.50), residues: 72
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.003   0.001   TYR A  89 
   ARG   0.001   0.000   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   TYR A  89 
   ARG   0.000   0.000   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.043 (Z=  2.705)
  Mean delta:    0.013 (Z=  0.672)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   107.86     4.74  1.00e+00  2.24e+01   4.7*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.16     6.04  1.30e+00  2.16e+01   4.6*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   129.82    -8.12  1.80e+00  2.03e+01   4.5*sigma
   A 132  LEU  N
   A 132  LEU  CA
   A 132  LEU  CB        110.50   117.94    -7.44  1.70e+00  1.92e+01   4.4*sigma
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   129.07    -7.37  1.80e+00  1.68e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.242 (Z=  4.737)
  Mean delta:    1.901 (Z=  1.048)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA          0.00   -21.08    21.08  5.00e+00  1.78e+01   4.2*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   159.30    20.70  5.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.067
  Max. delta:   90.869
  Mean delta:   17.857

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  CA
   A  85  LYS  N
   A  85  LYS  C
   A  85  LYS  CB          2.51    -2.05     4.56  2.00e-01  5.19e+02  22.8*sigma
   A 132  LEU  CA
   A 132  LEU  N
   A 132  LEU  C
   A 132  LEU  CB          2.51    -1.74     4.25  2.00e-01  4.51e+02  21.2*sigma

  Min. delta:    0.000
  Max. delta:    4.557
  Mean delta:    0.478

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.075       0.129      113.30   6.5*sigma

  Min. delta:    0.000
  Max. delta:    0.108
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.043   2242  Z= 0.478
    Angle     :  1.747   9.465   4079  Z= 0.776
    Chirality :  0.478   4.557    176
    Planarity :  0.013   0.088    327
    Dihedral  : 14.385  90.869    769
    Min Nonbonded Distance : 1.695
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  4.38 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  4.03 %
      Favored  : 92.74 %
    Cbeta Deviations :  2.27 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.96 (0.65), residues: 137
    helix: -0.21 (0.53), residues: 66
    sheet:  None (None), residues: 0
    loop : -0.99 (0.75), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.006   HIS A 135 
   PHE   0.053   0.016   PHE A  45 
   TYR   0.202   0.032   TYR A  68 
   ARG   0.089   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.006   HIS A 135 
   PHE   0.035   0.015   PHE A  45 
   TYR   0.169   0.039   TYR A  68 
   ARG   0.010   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  28  GLN

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  93.43 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     2
  Clashscore            =   4.06
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.79
  MolProbity score      =   1.62

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  92  THR  CB
   A  92  THR  OG1         1.43     1.34     0.10  1.60e-02  3.59e+01   6.0*sigma
   A  93  LEU  CA
   A  93  LEU  CB          1.53     1.63    -0.10  2.00e-02  2.32e+01   4.8*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.52    -0.07  1.60e-02  1.85e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.096 (Z=  5.994)
  Mean delta:    0.015 (Z=  0.788)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   140.16   -18.46  1.80e+00  1.05e+02  10.3*sigma
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        121.70   136.37   -14.67  1.80e+00  6.64e+01   8.1*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   134.61   -12.91  1.80e+00  5.14e+01   7.2*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30   123.17   -13.87  2.00e+00  4.81e+01   6.9*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   123.01   -12.91  1.90e+00  4.62e+01   6.8*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   118.86    -6.26  1.00e+00  3.92e+01   6.3*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N         116.20   128.20   -12.00  2.00e+00  3.60e+01   6.0*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   131.93   -10.23  1.80e+00  3.23e+01   5.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.85   -10.15  1.80e+00  3.18e+01   5.6*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   105.18    11.02  2.00e+00  3.04e+01   5.5*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   122.96   -11.66  2.30e+00  2.57e+01   5.1*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD2       110.70   125.62   -14.92  3.00e+00  2.47e+01   5.0*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   106.38     9.82  2.00e+00  2.41e+01   4.9*sigma
   A 138  HIS  O
   A 138  HIS  C
   A 139  HIS  N         123.00   115.37     7.63  1.60e+00  2.27e+01   4.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.29    -4.69  1.00e+00  2.20e+01   4.7*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   105.61     6.39  1.40e+00  2.08e+01   4.6*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   118.82    -9.72  2.20e+00  1.95e+01   4.4*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.21     4.39  1.00e+00  1.93e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.50     5.70  1.30e+00  1.93e+01   4.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   120.32    -8.72  2.00e+00  1.90e+01   4.4*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   116.88    -4.28  1.00e+00  1.83e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A  93  LEU  CA
   A  93  LEU  CB
   A  93  LEU  CG        116.30   130.60   -14.30  3.50e+00  1.67e+01   4.1*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   121.19    -7.29  1.80e+00  1.64e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.002)
  Max. delta:   18.461 (Z= 10.256)
  Mean delta:    2.460 (Z=  1.324)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   -48.06  -131.94  5.00e+00  6.96e+02  26.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -81.54   -98.46  5.00e+00  3.88e+02  19.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00    83.94    96.06  5.00e+00  3.69e+02  19.2*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   113.31    66.69  5.00e+00  1.78e+02  13.3*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   118.61    61.39  5.00e+00  1.51e+02  12.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -121.37   -58.63  5.00e+00  1.38e+02  11.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   127.65    52.35  5.00e+00  1.10e+02  10.5*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00  -142.78   -37.22  5.00e+00  5.54e+01   7.4*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00  -144.57   -35.43  5.00e+00  5.02e+01   7.1*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   145.92    34.08  5.00e+00  4.64e+01   6.8*sigma
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00   153.48    26.52  5.00e+00  2.81e+01   5.3*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -154.56   -25.44  5.00e+00  2.59e+01   5.1*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   155.71    24.29  5.00e+00  2.36e+01   4.9*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -156.11   -23.89  5.00e+00  2.28e+01   4.8*sigma
   A  50  TYR  CA
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        180.00   156.62    23.38  5.00e+00  2.19e+01   4.7*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -156.75   -23.25  5.00e+00  2.16e+01   4.7*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   156.76    23.24  5.00e+00  2.16e+01   4.6*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   156.91    23.09  5.00e+00  2.13e+01   4.6*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   157.01    22.99  5.00e+00  2.11e+01   4.6*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   157.18    22.82  5.00e+00  2.08e+01   4.6*sigma
   A   3  LEU  CA
   A   3  LEU  C
   A   4  ILE  N
   A   4  ILE  CA        180.00   157.56    22.44  5.00e+00  2.01e+01   4.5*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -157.83   -22.17  5.00e+00  1.97e+01   4.4*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00  -159.48   -20.52  5.00e+00  1.68e+01   4.1*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   159.57    20.43  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.009
  Max. delta:  131.938
  Mean delta:   18.751

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.67     5.32  2.00e-01  7.07e+02  26.6*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.75     5.26  2.00e-01  6.93e+02  26.3*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.35     4.78  2.00e-01  5.72e+02  23.9*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.00     4.52  2.00e-01  5.12e+02  22.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -2.04     4.47  2.00e-01  5.00e+02  22.4*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     1.01     1.50  2.00e-01  5.64e+01   7.5*sigma

  Min. delta:    0.000
  Max. delta:    5.319
  Mean delta:    0.845

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O
   A  80  GLY  N             0.074       0.129       55.14   6.4*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.047       0.081       44.56   4.0*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.042       0.080       34.99   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.130
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  88  ASP  HA , Angle N-CA-HA, observed: 95.708, delta from target: 14.292
   A  93  LEU  HG , Angle CB-CG-HG, observed: 93.872, delta from target: 15.128
   A  97  SER  HA , Angle C-CA-HA, observed: 85.447, delta from target: 23.553

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.096   2242  Z= 0.561
    Angle     :  2.190  23.553   4079  Z= 0.970
    Chirality :  0.845   5.319    176
    Planarity :  0.013   0.130    327
    Dihedral  : 15.229 131.938    769
    Min Nonbonded Distance : 1.553
  
  Molprobity Statistics.
    All-atom Clashscore : 12.17
    Ramachandran Plot:
      Outliers :  5.11 %
      Allowed  : 13.87 %
      Favored  : 81.02 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  5.65 %
      Favored  : 88.71 %
    Cbeta Deviations :  6.82 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 6.87 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.38 (0.67), residues: 137
    helix: -1.56 (0.51), residues: 72
    sheet:  None (None), residues: 0
    loop : -3.08 (0.82), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.088   0.019   PHE A  45 
   TYR   0.115   0.019   TYR A  50 
   ARG   0.026   0.006   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.035   0.012   PHE A  45 
   TYR   0.092   0.022   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Ramachandran outliers =  10.95 %
                favored =  81.75 %
  Rotamer outliers      =   8.87 %
  C-beta deviations     =    17
  Clashscore            =   7.21
  RMS(bonds)            =   0.0115
  RMS(angles)           =   2.58
  MolProbity score      =   2.83

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.92 %
                favored =  78.83 %
  Rotamer outliers      =  26.61 %
  C-beta deviations     =     0
  Clashscore            =  29.32
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.79

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  94.16 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     3
  Clashscore            =   1.80
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.75
  MolProbity score      =   1.72

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   5.11 %
                favored =  81.02 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     9
  Clashscore            =  12.17
  RMS(bonds)            =   0.0108
  RMS(angles)           =   2.19
  MolProbity score      =   2.89

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.516, 48.723, 42.827, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.826)
  Mean delta:    0.013 (Z=  0.674)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 109  LYS  C
   A 110  ASP  N
   A 110  ASP  CA        121.70   132.20   -10.50  1.80e+00  3.40e+01   5.8*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.80     4.80  1.00e+00  2.30e+01   4.8*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.99     4.61  1.00e+00  2.13e+01   4.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   125.43    -9.23  2.00e+00  2.13e+01   4.6*sigma
   A  92  THR  O
   A  92  THR  C
   A  93  LEU  N         123.00   115.98     7.02  1.60e+00  1.92e+01   4.4*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.30     4.30  1.00e+00  1.85e+01   4.3*sigma
   A 110  ASP  N
   A 110  ASP  CA
   A 110  ASP  C         111.00   122.63   -11.63  2.80e+00  1.72e+01   4.2*sigma
   A 108  ILE  CA
   A 108  ILE  CB
   A 108  ILE  CG1       110.40   117.42    -7.02  1.70e+00  1.71e+01   4.1*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   121.27    -7.37  1.80e+00  1.68e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   11.629 (Z=  5.831)
  Mean delta:    2.105 (Z=  1.140)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   144.97    35.03  5.00e+00  4.91e+01   7.0*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   153.87    26.13  5.00e+00  2.73e+01   5.2*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -158.20   -21.80  5.00e+00  1.90e+01   4.4*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -158.47   -21.53  5.00e+00  1.85e+01   4.3*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -159.19   -20.81  5.00e+00  1.73e+01   4.2*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   159.91    20.09  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.033
  Max. delta:   87.112
  Mean delta:   15.273

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.34     4.85  2.00e-01  5.87e+02  24.2*sigma
   A 109  LYS  CA
   A 109  LYS  N
   A 109  LYS  C
   A 109  LYS  CB          2.51     1.35     1.16  2.00e-01  3.38e+01   5.8*sigma

  Min. delta:    0.001
  Max. delta:    4.846
  Mean delta:    0.393

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.094       0.164      178.60   8.2*sigma
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.061       0.109       73.70   5.5*sigma

  Min. delta:    0.000
  Max. delta:    0.109
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 110  ASP  HA , Angle C-CA-HA, observed: 94.112, delta from target: 14.888
   A 109  LYS  HA , Angle C-CA-HA, observed: 93.675, delta from target: 15.325

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.480
    Angle     :  1.907  15.325   4079  Z= 0.842
    Chirality :  0.393   4.846    176
    Planarity :  0.014   0.088    327
    Dihedral  : 13.994  87.112    769
    Min Nonbonded Distance : 1.721
  
  Molprobity Statistics.
    All-atom Clashscore : 2.25
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  6.57 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  5.65 %
      Favored  : 91.94 %
    Cbeta Deviations :  2.27 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.79 (0.62), residues: 137
    helix: -0.90 (0.52), residues: 66
    sheet:  None (None), residues: 0
    loop : -1.43 (0.71), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.019   0.006   HIS A 136 
   PHE   0.025   0.007   PHE A  45 
   TYR   0.209   0.041   TYR A  81 
   ARG   0.095   0.014   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.019   0.006   HIS A 136 
   PHE   0.024   0.007   PHE A  45 
   TYR   0.170   0.046   TYR A  81 
   ARG   0.005   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN
   A 139  HIS

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 463
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.45e+00
  bond model="   9" pdb=" NE  ARG A 127 "
       model="   9" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 8.10e-02
  bond model="   9" pdb=" CZ  ARG A 127 "
       model="   9" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 6.78e-02
  bond model="   9" pdb=" CZ  ARG A  58 "
       model="   9" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.36e-02
  bond model="   9" pdb=" CZ  ARG A  58 "
       model="   9" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.29e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.89 -   106.89: 69
      106.89 -   112.90: 2716
      112.90 -   118.90: 426
      118.90 -   124.90: 824
      124.90 -   130.91: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A  54 "
        model="   9" pdb=" CA  PRO A  54 "
        model="   9" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.60e+00
  angle model="   9" pdb=" CB  PRO A  22 "
        model="   9" pdb=" CA  PRO A  22 "
        model="   9" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A  52 "
        model="   9" pdb=" CA  PRO A  52 "
        model="   9" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   9" pdb=" CB  PRO A   6 "
        model="   9" pdb=" CA  PRO A   6 "
        model="   9" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   9" pdb=" CB  PRO A 102 "
        model="   9" pdb=" CA  PRO A 102 "
        model="   9" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 871
       17.93 -    35.86: 91
       35.86 -    53.80: 43
       53.80 -    71.73: 24
       71.73 -    89.66: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CB  GLU A  49 "
           model="   9" pdb=" CG  GLU A  49 "
           model="   9" pdb=" CD  GLU A  49 "
           model="   9" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.66   89.66     1      3.00e+01 1.11e-03 1.06e+01
  dihedral model="   9" pdb=" CB  GLU A  84 "
           model="   9" pdb=" CG  GLU A  84 "
           model="   9" pdb=" CD  GLU A  84 "
           model="   9" pdb=" OE1 GLU A  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.10   88.10     1      3.00e+01 1.11e-03 1.03e+01
  dihedral model="   9" pdb=" CA  LEU A   3 "
           model="   9" pdb=" CB  LEU A   3 "
           model="   9" pdb=" CG  LEU A   3 "
           model="   9" pdb=" CD1 LEU A   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.73   59.27     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 96
       0.019 -    0.038: 55
       0.038 -    0.056: 6
       0.056 -    0.075: 0
       0.075 -    0.094: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A  51 "
            model="   9" pdb=" N   ILE A  51 "
            model="   9" pdb=" C   ILE A  51 "
            model="   9" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.20e-01
  chirality model="   9" pdb=" CA  ILE A 131 "
            model="   9" pdb=" N   ILE A 131 "
            model="   9" pdb=" C   ILE A 131 "
            model="   9" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.20e-01
  chirality model="   9" pdb=" CA  ILE A  77 "
            model="   9" pdb=" N   ILE A  77 "
            model="   9" pdb=" C   ILE A  77 "
            model="   9" pdb=" CB  ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A 111 "    0.001 2.00e-02 2.50e+03   1.31e-03 5.13e-02
        model="   9" pdb=" CG  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  89 "   -0.000 2.00e-02 2.50e+03   1.17e-03 4.07e-02
        model="   9" pdb=" CG  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  89 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A 105 "    0.000 2.00e-02 2.50e+03   1.05e-03 3.34e-02
        model="   9" pdb=" CG  TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A 105 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A 105 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 194
        2.18 -     2.78: 4618
        2.78 -     3.39: 5715
        3.39 -     3.99: 7139
        3.99 -     4.60: 10669
  Nonbonded interactions: 28335
  Sorted by model distance:
  nonbonded model="   9" pdb="HD13 LEU A   3 "
            model="   9" pdb="HD22 LEU A  53 "
     model   vdw
     1.570 2.440
  nonbonded model="   9" pdb="HD23 LEU A   9 "
            model="   9" pdb="HD22 LEU A  26 "
     model   vdw
     1.582 2.440
  nonbonded model="   9" pdb="HG23 ILE A  37 "
            model="   9" pdb="HD13 ILE A 108 "
     model   vdw
     1.653 2.440
  nonbonded model="   9" pdb="HG23 ILE A  71 "
            model="   9" pdb="HD22 LEU A  99 "
     model   vdw
     1.696 2.440
  nonbonded model="   9" pdb="HG22 ILE A  78 "
            model="   9" pdb=" H   GLY A  80 "
     model   vdw
     1.725 2.270
  ... (remaining 28330 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.073 (Z=  3.497)
  Mean delta:    0.014 (Z=  0.745)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    93.15    16.95  1.90e+00  7.95e+01   8.9*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   135.01   -13.31  1.80e+00  5.47e+01   7.4*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   134.79   -13.09  1.80e+00  5.29e+01   7.3*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   133.69   -11.99  1.80e+00  4.44e+01   6.7*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   102.86     9.14  1.40e+00  4.26e+01   6.5*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   119.03    -6.43  1.00e+00  4.13e+01   6.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   124.42   -12.82  2.00e+00  4.11e+01   6.4*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   121.33   -11.23  1.90e+00  3.49e+01   5.9*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   132.09   -10.39  1.80e+00  3.33e+01   5.8*sigma
   A 119  LEU  N
   A 119  LEU  CA
   A 119  LEU  CB        110.50   101.15     9.35  1.70e+00  3.03e+01   5.5*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   119.62    -9.52  1.90e+00  2.51e+01   5.0*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.55    -4.95  1.00e+00  2.45e+01   5.0*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   115.13     7.87  1.60e+00  2.42e+01   4.9*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   108.19    -5.19  1.10e+00  2.23e+01   4.7*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   130.06    -8.36  1.80e+00  2.16e+01   4.6*sigma
   A 119  LEU  C
   A 119  LEU  CA
   A 119  LEU  CB        110.10   118.83    -8.73  1.90e+00  2.11e+01   4.6*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   118.17    -7.77  1.70e+00  2.09e+01   4.6*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   118.09    -7.59  1.70e+00  1.99e+01   4.5*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   117.83    -7.33  1.70e+00  1.86e+01   4.3*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.25    -5.85  1.40e+00  1.75e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.73e+01   4.2*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   123.11    -6.21  1.50e+00  1.72e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.52     4.08  1.00e+00  1.66e+01   4.1*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   129.01    -7.31  1.80e+00  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   16.945 (Z=  8.919)
  Mean delta:    2.394 (Z=  1.313)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -112.39   -67.61  5.00e+00  1.83e+02  13.5*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -113.29   -66.71  5.00e+00  1.78e+02  13.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -113.74   -66.26  5.00e+00  1.76e+02  13.3*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -119.08   -60.92  5.00e+00  1.48e+02  12.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -121.28   -58.72  5.00e+00  1.38e+02  11.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   125.72    54.28  5.00e+00  1.18e+02  10.9*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   129.69    50.31  5.00e+00  1.01e+02  10.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -132.09   -47.91  5.00e+00  9.18e+01   9.6*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   137.53    42.47  5.00e+00  7.21e+01   8.5*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   141.10    38.90  5.00e+00  6.05e+01   7.8*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   146.88    33.12  5.00e+00  4.39e+01   6.6*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -147.12   -32.88  5.00e+00  4.33e+01   6.6*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   147.14    32.86  5.00e+00  4.32e+01   6.6*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -152.02   -27.98  5.00e+00  3.13e+01   5.6*sigma
   A  46  SER  CA
   A  46  SER  C
   A  47  ASP  N
   A  47  ASP  CA        180.00   158.32    21.68  5.00e+00  1.88e+01   4.3*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -158.82   -21.18  5.00e+00  1.79e+01   4.2*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -159.37   -20.63  5.00e+00  1.70e+01   4.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -159.75   -20.25  5.00e+00  1.64e+01   4.0*sigma
   A  42  GLY  CA
   A  42  GLY  C
   A  43  HIS  N
   A  43  HIS  CA        180.00   159.93    20.07  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.018
  Max. delta:   89.776
  Mean delta:   18.085

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.13     5.64  2.00e-01  7.96e+02  28.2*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.67     5.32  2.00e-01  7.07e+02  26.6*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -2.64     5.16  2.00e-01  6.64e+02  25.8*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.48     5.12  2.00e-01  6.56e+02  25.6*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.44     4.87  2.00e-01  5.94e+02  24.4*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.54     3.97  2.00e-01  3.94e+02  19.9*sigma

  Min. delta:    0.001
  Max. delta:    5.642
  Mean delta:    0.943

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CD            0.153       0.265       37.66   5.3*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.065       0.095       83.89   4.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O
   A  93  LEU  N             0.052       0.090       26.88   4.5*sigma

  Min. delta:    0.000
  Max. delta:    0.153
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  51  ILE  HA , Angle C-CA-HA, observed: 95.488, delta from target: 13.512
   A  79  LYS  HA , Angle C-CA-HA, observed: 125.010, delta from target: -16.010
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.743, delta from target: 16.257

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.073   2242  Z= 0.531
    Angle     :  2.132  16.945   4079  Z= 0.957
    Chirality :  0.943   5.642    176
    Planarity :  0.015   0.153    327
    Dihedral  : 14.604  89.776    769
    Min Nonbonded Distance : 1.546
  
  Molprobity Statistics.
    All-atom Clashscore : 16.68
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  8.03 %
      Favored  : 87.59 %
    Rotamer:
      Outliers :  8.06 %
      Allowed  :  4.03 %
      Favored  : 87.90 %
    Cbeta Deviations :  6.82 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 9.16 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.98 (0.60), residues: 137
    helix: -2.22 (0.48), residues: 75
    sheet:  None (None), residues: 0
    loop : -3.17 (0.70), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.004   HIS A  43 
   PHE   0.064   0.012   PHE A  67 
   TYR   0.156   0.023   TYR A  89 
   ARG   0.032   0.006   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.004   HIS A  43 
   PHE   0.024   0.006   PHE A  67 
   TYR   0.123   0.027   TYR A  89 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  91.97 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     3
  Clashscore            =   2.25
  RMS(bonds)            =   0.0094
  RMS(angles)           =   1.91
  MolProbity score      =   1.78

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 126  VAL  C
   A 127  ARG  N           1.33     1.26     0.07  1.40e-02  2.60e+01   5.1*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.59    -0.08  1.80e-02  1.90e+01   4.4*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.54    -0.08  1.90e-02  1.70e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.078 (Z=  5.102)
  Mean delta:    0.016 (Z=  0.827)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   132.37   -18.47  1.80e+00  1.05e+02  10.3*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   103.39    18.31  1.80e+00  1.03e+02  10.2*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20    97.76    18.44  2.00e+00  8.50e+01   9.2*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   136.01   -14.31  1.80e+00  6.32e+01   8.0*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   123.22   -12.72  1.70e+00  5.60e+01   7.5*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   133.47   -12.67  1.70e+00  5.56e+01   7.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.75   -10.85  1.50e+00  5.23e+01   7.2*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   134.24   -12.54  1.80e+00  4.85e+01   7.0*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   134.21   -12.51  1.80e+00  4.83e+01   7.0*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   121.51   -11.01  1.70e+00  4.19e+01   6.5*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   120.87   -10.47  1.70e+00  3.79e+01   6.2*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   121.65   -11.55  1.90e+00  3.70e+01   6.1*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   120.72   -10.32  1.70e+00  3.69e+01   6.1*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   110.83    10.87  1.80e+00  3.65e+01   6.0*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.33   -10.63  1.80e+00  3.49e+01   5.9*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   120.48    -9.98  1.70e+00  3.45e+01   5.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.40    -5.80  1.00e+00  3.36e+01   5.8*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   131.90   -10.20  1.80e+00  3.21e+01   5.7*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   119.60    -9.20  1.70e+00  2.93e+01   5.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.97   -10.37  2.00e+00  2.69e+01   5.2*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   119.12    -8.62  1.70e+00  2.57e+01   5.1*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  CB        110.50   118.91    -8.41  1.70e+00  2.45e+01   4.9*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   118.76    -8.26  1.70e+00  2.36e+01   4.9*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   129.72    -8.02  1.80e+00  1.99e+01   4.5*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   118.24    -4.44  1.00e+00  1.97e+01   4.4*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   123.42   -12.42  2.80e+00  1.97e+01   4.4*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40   103.81     6.59  1.50e+00  1.93e+01   4.4*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.49     5.71  1.30e+00  1.93e+01   4.4*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   118.34    -8.24  1.90e+00  1.88e+01   4.3*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   129.48    -7.78  1.80e+00  1.87e+01   4.3*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   116.87    -4.27  1.00e+00  1.82e+01   4.3*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   129.36    -7.66  1.80e+00  1.81e+01   4.3*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   120.02    -8.42  2.00e+00  1.77e+01   4.2*sigma
   A  71  ILE  N
   A  71  ILE  CA
   A  71  ILE  CB        111.50   104.41     7.09  1.70e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50   104.49     7.01  1.70e+00  1.70e+01   4.1*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   129.13    -7.43  1.80e+00  1.70e+01   4.1*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   103.58     7.82  1.90e+00  1.69e+01   4.1*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.15    -5.75  1.40e+00  1.69e+01   4.1*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   121.19    -7.29  1.80e+00  1.64e+01   4.0*sigma
   A  43  HIS  ND1
   A  43  HIS  CG
   A  43  HIS  CD2       106.10   110.12    -4.02  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   18.467 (Z= 10.260)
  Mean delta:    2.824 (Z=  1.537)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   -76.42  -103.58  5.00e+00  4.29e+02  20.7*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    78.20   101.80  5.00e+00  4.15e+02  20.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    93.72    86.28  5.00e+00  2.98e+02  17.3*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00    95.42    84.58  5.00e+00  2.86e+02  16.9*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   104.53    75.47  5.00e+00  2.28e+02  15.1*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -104.88   -75.12  5.00e+00  2.26e+02  15.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -108.44   -71.56  5.00e+00  2.05e+02  14.3*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00  -112.44   -67.56  5.00e+00  1.83e+02  13.5*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   119.77    60.23  5.00e+00  1.45e+02  12.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   122.19    57.81  5.00e+00  1.34e+02  11.6*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -134.37   -45.63  5.00e+00  8.33e+01   9.1*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   140.80    39.20  5.00e+00  6.15e+01   7.8*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -140.87   -39.13  5.00e+00  6.12e+01   7.8*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -147.70   -32.30  5.00e+00  4.17e+01   6.5*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   150.42    29.58  5.00e+00  3.50e+01   5.9*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -151.83   -28.17  5.00e+00  3.17e+01   5.6*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   151.91    28.09  5.00e+00  3.16e+01   5.6*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00   153.06    26.94  5.00e+00  2.90e+01   5.4*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -155.14   -24.86  5.00e+00  2.47e+01   5.0*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -156.90   -23.10  5.00e+00  2.14e+01   4.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   158.05    21.95  5.00e+00  1.93e+01   4.4*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   158.38    21.62  5.00e+00  1.87e+01   4.3*sigma
   A  43  HIS  CA
   A  43  HIS  C
   A  44  ASP  N
   A  44  ASP  CA        180.00  -158.43   -21.57  5.00e+00  1.86e+01   4.3*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00  -158.97   -21.03  5.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.018
  Max. delta:  103.578
  Mean delta:   20.862

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -2.85     5.33  2.00e-01  7.12e+02  26.7*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.46     5.10  2.00e-01  6.51e+02  25.5*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.50     5.02  2.00e-01  6.29e+02  25.1*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -2.43     4.94  2.00e-01  6.11e+02  24.7*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.33     4.77  2.00e-01  5.69e+02  23.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.93     3.37  2.00e-01  2.83e+02  16.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -0.83     3.26  2.00e-01  2.66e+02  16.3*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     0.14     2.37  2.00e-01  1.40e+02  11.8*sigma
   A 126  VAL  CB
   A 126  VAL  CA
   A 126  VAL  CG1
   A 126  VAL  CG2        -2.63    -1.51    -1.12  2.00e-01  3.15e+01   5.6*sigma
   A 130  SER  CA
   A 130  SER  N
   A 130  SER  C
   A 130  SER  CB          2.51     1.48     1.03  2.00e-01  2.64e+01   5.1*sigma

  Min. delta:    0.001
  Max. delta:    5.335
  Mean delta:    0.961

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.081       0.116      131.74   5.8*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.052       0.100       54.40   5.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O
   A  91  TYR  N             0.048       0.083       23.06   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.081
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 126  VAL  HA , Angle N-CA-HA, observed: 97.673, delta from target: 12.327
   A 130  SER  HA , Angle N-CA-HA, observed: 96.697, delta from target: 13.303
   A  77  ILE  HA , Angle C-CA-HA, observed: 95.278, delta from target: 13.722
   A  78  ILE  HA , Angle N-CA-HA, observed: 95.098, delta from target: 14.902
   A 122  ILE  HB , Angle CA-CB-HB, observed: 92.333, delta from target: 16.667
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.909, delta from target: 17.091
   A  51  ILE  HA , Angle CB-CA-HA, observed: 91.493, delta from target: 17.507
   A  78  ILE  HA , Angle C-CA-HA, observed: 90.704, delta from target: 18.296
   A 126  VAL  HB , Angle CA-CB-HB, observed: 89.220, delta from target: 19.780
   A  89  TYR  HA , Angle N-CA-HA, observed: 90.182, delta from target: 19.818
   A 127  ARG  HA , Angle CB-CA-HA, observed: 87.500, delta from target: 21.500
   A  81  TYR  HA , Angle N-CA-HA, observed: 52.507, delta from target: 57.493

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.078   2242  Z= 0.589
    Angle     :  2.653  57.493   4079  Z= 1.157
    Chirality :  0.961   5.335    176
    Planarity :  0.013   0.109    327
    Dihedral  : 16.797 103.578    769
    Min Nonbonded Distance : 1.673
  
  Molprobity Statistics.
    All-atom Clashscore : 11.72
    Ramachandran Plot:
      Outliers :  8.76 %
      Allowed  :  9.49 %
      Favored  : 81.75 %
    Rotamer:
      Outliers : 11.29 %
      Allowed  :  6.45 %
      Favored  : 82.26 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 10.69 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.24 (0.67), residues: 137
    helix: -1.74 (0.54), residues: 69
    sheet:  None (None), residues: 0
    loop : -2.60 (0.78), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A 136 
   PHE   0.088   0.018   PHE A  67 
   TYR   0.221   0.028   TYR A  81 
   ARG   0.028   0.005   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A 136 
   PHE   0.068   0.018   PHE A  67 
   TYR   0.122   0.028   TYR A  81 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   4.38 %
                favored =  87.59 %
  Rotamer outliers      =   8.06 %
  C-beta deviations     =     9
  Clashscore            =  16.68
  RMS(bonds)            =   0.0103
  RMS(angles)           =   2.13
  MolProbity score      =   3.02

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   8.76 %
                favored =  81.75 %
  Rotamer outliers      =  11.29 %
  C-beta deviations     =    16
  Clashscore            =  11.72
  RMS(bonds)            =   0.0112
  RMS(angles)           =   2.65
  MolProbity score      =   3.10

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU  132": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.562)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.593 (Z=  1.351)
  Mean delta:    0.376 (Z=  0.206)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   84.287
  Mean delta:   23.089

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.094
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.045
    Angle     :  0.979   4.824   4077  Z= 0.341
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.024  84.287    768
    Min Nonbonded Distance : 1.572
  
  Molprobity Statistics.
    All-atom Clashscore : 19.85
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  : 15.33 %
      Favored  : 78.10 %
    Rotamer:
      Outliers : 30.65 %
      Allowed  : 14.52 %
      Favored  : 54.84 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.23 (0.45), residues: 137
    helix: -3.80 (0.38), residues: 55
    sheet:  None (None), residues: 0
    loop : -4.67 (0.48), residues: 82
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 136 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.003   0.001   TYR A 105 
   ARG   0.001   0.000   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 136 
   PHE   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   TYR A 105 
   ARG   0.000   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 135  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.038 (Z=  2.838)
  Mean delta:    0.013 (Z=  0.685)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   134.18   -12.48  1.80e+00  4.81e+01   6.9*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   120.61   -10.51  1.90e+00  3.06e+01   5.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.63     4.97  1.00e+00  2.47e+01   5.0*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   117.72    -7.22  1.70e+00  1.80e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   12.482 (Z=  6.935)
  Mean delta:    1.964 (Z=  1.060)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -132.06   -47.94  5.00e+00  9.19e+01   9.6*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -138.78   -41.22  5.00e+00  6.80e+01   8.2*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -142.63   -37.37  5.00e+00  5.59e+01   7.5*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -157.82   -22.18  5.00e+00  1.97e+01   4.4*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -159.84   -20.16  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.030
  Max. delta:   63.422
  Mean delta:   14.970

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.533
  Mean delta:    0.105

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.089       0.155      159.82   7.7*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.076       0.133      115.94   6.6*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.062       0.108       76.35   5.4*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.052       0.092       54.62   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.089
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  93  LEU  HA , Angle C-CA-HA, observed: 95.376, delta from target: 13.624

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.488
    Angle     :  1.807  13.624   4079  Z= 0.791
    Chirality :  0.105   0.533    176
    Planarity :  0.013   0.083    327
    Dihedral  : 13.158  63.422    769
    Min Nonbonded Distance : 1.547
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  3.23 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.97 (0.67), residues: 137
    helix: -1.07 (0.46), residues: 71
    sheet:  None (None), residues: 0
    loop :  0.09 (0.87), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A 136 
   PHE   0.103   0.020   PHE A  67 
   TYR   0.186   0.034   TYR A  50 
   ARG   0.071   0.014   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A 136 
   PHE   0.050   0.016   PHE A  67 
   TYR   0.155   0.037   TYR A  50 
   ARG   0.009   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

  Ramachandran outliers =   6.57 %
                favored =  78.10 %
  Rotamer outliers      =  30.65 %
  C-beta deviations     =     0
  Clashscore            =  19.85
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.68

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.790)
  Mean delta:    0.013 (Z=  0.683)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        121.70   132.96   -11.26  1.80e+00  3.91e+01   6.3*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   132.01   -10.31  1.80e+00  3.28e+01   5.7*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.36     4.24  1.00e+00  1.80e+01   4.2*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.76     5.44  1.30e+00  1.75e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   11.258 (Z=  6.255)
  Mean delta:    1.997 (Z=  1.098)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   152.98    27.02  5.00e+00  2.92e+01   5.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -154.05   -25.95  5.00e+00  2.69e+01   5.2*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -155.65   -24.35  5.00e+00  2.37e+01   4.9*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   157.35    22.65  5.00e+00  2.05e+01   4.5*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   159.01    20.99  5.00e+00  1.76e+01   4.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   159.14    20.86  5.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.077
  Max. delta:   87.679
  Mean delta:   18.039

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 120  GLU  CA
   A 120  GLU  N
   A 120  GLU  C
   A 120  GLU  CB          2.51    -2.12     4.63  2.00e-01  5.36e+02  23.2*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -1.47     3.98  2.00e-01  3.96e+02  19.9*sigma

  Min. delta:    0.000
  Max. delta:    4.631
  Mean delta:    0.471

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.043       0.081       37.47   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.140
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 127  ARG  HA , Angle N-CA-HA, observed: 96.276, delta from target: 13.724

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.487
    Angle     :  1.850  13.724   4079  Z= 0.817
    Chirality :  0.471   4.631    176
    Planarity :  0.014   0.142    327
    Dihedral  : 14.646  87.679    769
    Min Nonbonded Distance : 1.670
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  8.03 %
      Favored  : 90.51 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  4.03 %
      Favored  : 89.52 %
    Cbeta Deviations :  1.52 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.60 (0.68), residues: 137
    helix: -0.22 (0.61), residues: 61
    sheet:  None (None), residues: 0
    loop : -1.83 (0.72), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 139 
   PHE   0.043   0.013   PHE A  15 
   TYR   0.314   0.032   TYR A  81 
   ARG   0.113   0.015   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 139 
   PHE   0.026   0.010   PHE A  15 
   TYR   0.124   0.025   TYR A  81 
   ARG   0.018   0.004   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.00 %
                favored =  94.89 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     1
  Clashscore            =   4.51
  RMS(bonds)            =   0.0094
  RMS(angles)           =   1.81
  MolProbity score      =   1.87

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  90.51 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =     2
  Clashscore            =   4.51
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.85
  MolProbity score      =   2.38

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.32     0.20  2.10e-02  9.09e+01   9.5*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.66    -0.15  1.80e-02  6.71e+01   8.2*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.57    -0.12  1.60e-02  5.88e+01   7.7*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.60    -0.14  1.90e-02  5.50e+01   7.4*sigma
   A 125  LYS  CA
   A 125  LYS  C           1.52     1.37     0.16  2.10e-02  5.49e+01   7.4*sigma
   A 124  ALA  C
   A 125  LYS  N           1.33     1.42    -0.09  1.40e-02  4.22e+01   6.5*sigma
   A  93  LEU  C
   A  94  GLY  N           1.33     1.25     0.08  1.40e-02  3.47e+01   5.9*sigma
   A  79  LYS  CA
   A  79  LYS  CB          1.53     1.65    -0.12  2.00e-02  3.36e+01   5.8*sigma
   A  94  GLY  N
   A  94  GLY  CA          1.45     1.36     0.09  1.60e-02  3.10e+01   5.6*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.40    -0.08  1.40e-02  2.94e+01   5.4*sigma
   A  90  SER  N
   A  90  SER  CA          1.46     1.55    -0.09  1.90e-02  2.22e+01   4.7*sigma
   A  78  ILE  CA
   A  78  ILE  CB          1.54     1.66    -0.12  2.70e-02  1.86e+01   4.3*sigma
   A  93  LEU  N
   A  93  LEU  CA          1.46     1.38     0.08  1.90e-02  1.64e+01   4.1*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.61    -0.08  2.10e-02  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.200 (Z=  9.535)
  Mean delta:    0.021 (Z=  1.083)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   150.14   -38.74  1.90e+00  4.16e+02  20.4*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   139.46   -28.16  2.30e+00  1.50e+02  12.2*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   100.35    21.35  1.80e+00  1.41e+02  11.9*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  CB        111.50   130.58   -19.08  1.70e+00  1.26e+02  11.2*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   102.37    19.33  1.80e+00  1.15e+02  10.7*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   129.78   -19.68  1.90e+00  1.07e+02  10.4*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   140.21   -18.51  1.80e+00  1.06e+02  10.3*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   126.25   -15.75  1.70e+00  8.59e+01   9.3*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50    95.85    15.65  1.70e+00  8.48e+01   9.2*sigma
   A 125  LYS  C
   A 125  LYS  CA
   A 125  LYS  CB        110.10   125.52   -15.42  1.90e+00  6.59e+01   8.1*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   135.78   -14.08  1.80e+00  6.12e+01   7.8*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   107.68    14.02  1.80e+00  6.06e+01   7.8*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   124.75   -14.65  1.90e+00  5.95e+01   7.7*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   129.31   -15.21  2.00e+00  5.78e+01   7.6*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00    89.98    21.02  2.80e+00  5.64e+01   7.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.00   -11.10  1.50e+00  5.47e+01   7.4*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    90.80    20.20  2.80e+00  5.20e+01   7.2*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   134.31   -12.61  1.80e+00  4.91e+01   7.0*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   134.29   -12.59  1.80e+00  4.89e+01   7.0*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  C         111.00    91.55    19.45  2.80e+00  4.82e+01   6.9*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   129.58   -13.38  2.00e+00  4.47e+01   6.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   133.48   -11.78  1.80e+00  4.28e+01   6.5*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   121.39   -10.89  1.70e+00  4.11e+01   6.4*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   133.22   -11.52  1.80e+00  4.10e+01   6.4*sigma
   A 124  ALA  O
   A 124  ALA  C
   A 125  LYS  N         123.00   133.19   -10.19  1.60e+00  4.06e+01   6.4*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  C         111.00    93.18    17.82  2.80e+00  4.05e+01   6.4*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   133.06   -11.36  1.80e+00  3.99e+01   6.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.97   -11.27  1.80e+00  3.92e+01   6.3*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   111.10    10.60  1.80e+00  3.47e+01   5.9*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   120.34    -9.94  1.70e+00  3.42e+01   5.8*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   120.43    -9.93  1.70e+00  3.41e+01   5.8*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   120.29    -9.89  1.70e+00  3.39e+01   5.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.29    -5.69  1.00e+00  3.24e+01   5.7*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   126.76   -15.76  2.80e+00  3.17e+01   5.6*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   111.46     9.34  1.70e+00  3.02e+01   5.5*sigma
   A 135  HIS  CA
   A 135  HIS  CB
   A 135  HIS  CG        113.80   119.17    -5.37  1.00e+00  2.88e+01   5.4*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    99.99    10.11  1.90e+00  2.83e+01   5.3*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   101.46     9.04  1.70e+00  2.83e+01   5.3*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   101.35    10.25  2.00e+00  2.63e+01   5.1*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   130.65    -8.95  1.80e+00  2.47e+01   5.0*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.43    -9.83  2.00e+00  2.41e+01   4.9*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   130.41    -8.71  1.80e+00  2.34e+01   4.8*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N         116.20   106.52     9.68  2.00e+00  2.34e+01   4.8*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   117.44    -4.84  1.00e+00  2.34e+01   4.8*sigma
   A  78  ILE  CB
   A  78  ILE  CG1
   A  78  ILE  CD1       113.80   123.81   -10.01  2.10e+00  2.27e+01   4.8*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   117.65    -7.15  1.50e+00  2.27e+01   4.8*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    97.73    13.27  2.80e+00  2.25e+01   4.7*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   101.21     8.89  1.90e+00  2.19e+01   4.7*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   118.37    -7.87  1.70e+00  2.14e+01   4.6*sigma
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        121.70   113.38     8.32  1.80e+00  2.14e+01   4.6*sigma
   A  76  SER  CA
   A  76  SER  C
   A  76  SER  O         120.80   113.07     7.73  1.70e+00  2.07e+01   4.5*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   117.09    -4.49  1.00e+00  2.02e+01   4.5*sigma
   A  79  LYS  CG
   A  79  LYS  CD
   A  79  LYS  CE        111.30   121.55   -10.25  2.30e+00  1.99e+01   4.5*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   123.48   -12.48  2.80e+00  1.99e+01   4.5*sigma
   A  93  LEU  O
   A  93  LEU  C
   A  94  GLY  N         123.00   115.87     7.13  1.60e+00  1.99e+01   4.5*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   123.38   -12.38  2.80e+00  1.96e+01   4.4*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N         116.20   107.37     8.83  2.00e+00  1.95e+01   4.4*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   116.00     7.00  1.60e+00  1.91e+01   4.4*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   129.56    -7.86  1.80e+00  1.91e+01   4.4*sigma
   A 133  GLU  N
   A 133  GLU  CA
   A 133  GLU  CB        110.50   103.23     7.27  1.70e+00  1.83e+01   4.3*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   102.24     7.86  1.90e+00  1.71e+01   4.1*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   129.13    -7.43  1.80e+00  1.70e+01   4.1*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N         116.20   108.00     8.20  2.00e+00  1.68e+01   4.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   103.53     6.97  1.70e+00  1.68e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   121.24    -7.34  1.80e+00  1.66e+01   4.1*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N         116.20   108.17     8.03  2.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   38.739 (Z= 20.389)
  Mean delta:    3.609 (Z=  1.886)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -45.18  -134.82  5.00e+00  7.27e+02  27.0*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   -73.20  -106.80  5.00e+00  4.56e+02  21.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   -73.58  -106.42  5.00e+00  4.53e+02  21.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    83.44    96.56  5.00e+00  3.73e+02  19.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    86.30    93.70  5.00e+00  3.51e+02  18.7*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00    95.74    84.26  5.00e+00  2.84e+02  16.9*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -102.13   -77.87  5.00e+00  2.43e+02  15.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   103.88    76.12  5.00e+00  2.32e+02  15.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -113.67   -66.33  5.00e+00  1.76e+02  13.3*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -114.73   -65.27  5.00e+00  1.70e+02  13.1*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -120.39   -59.61  5.00e+00  1.42e+02  11.9*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -128.28   -51.72  5.00e+00  1.07e+02  10.3*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   132.66    47.34  5.00e+00  8.96e+01   9.5*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   135.87    44.13  5.00e+00  7.79e+01   8.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   139.02    40.98  5.00e+00  6.72e+01   8.2*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   140.04    39.96  5.00e+00  6.39e+01   8.0*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   142.17    37.83  5.00e+00  5.72e+01   7.6*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00  -142.40   -37.60  5.00e+00  5.65e+01   7.5*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -145.71   -34.29  5.00e+00  4.70e+01   6.9*sigma
   A  70  LEU  CA
   A  70  LEU  C
   A  71  ILE  N
   A  71  ILE  CA        180.00   146.57    33.43  5.00e+00  4.47e+01   6.7*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -148.69   -31.31  5.00e+00  3.92e+01   6.3*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   149.90    30.10  5.00e+00  3.62e+01   6.0*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   151.12    28.88  5.00e+00  3.34e+01   5.8*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   159.63    20.37  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.011
  Max. delta:  134.816
  Mean delta:   22.456

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.72     6.23  2.00e-01  9.72e+02  31.2*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.64     5.29  2.00e-01  6.99e+02  26.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.35     4.91  2.00e-01  6.02e+02  24.5*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.18     4.69  2.00e-01  5.51e+02  23.5*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.17     4.68  2.00e-01  5.49e+02  23.4*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -1.95     4.46  2.00e-01  4.97e+02  22.3*sigma
   A 130  SER  CA
   A 130  SER  N
   A 130  SER  C
   A 130  SER  CB          2.51    -1.94     4.45  2.00e-01  4.95e+02  22.2*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.86     4.37  2.00e-01  4.77e+02  21.8*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -1.84     4.28  2.00e-01  4.58e+02  21.4*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -1.15     3.66  2.00e-01  3.34e+02  18.3*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.11     3.54  2.00e-01  3.13e+02  17.7*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -0.60     3.04  2.00e-01  2.30e+02  15.2*sigma

  Min. delta:    0.000
  Max. delta:    6.234
  Mean delta:    1.195

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.060       0.110       71.24   5.5*sigma
   A 128  MET  CA
   A 128  MET  C
   A 128  MET  O
   A 129  ARG  N             0.055       0.095       30.26   4.8*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.045       0.086       40.83   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.085
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  90  SER  HA , Angle CB-CA-HA, observed: 96.757, delta from target: 12.243
   A 126  VAL  HA , Angle C-CA-HA, observed: 96.713, delta from target: 12.287
   A 130  SER  HA , Angle C-CA-HA, observed: 96.712, delta from target: 12.288
   A 124  ALA  HA , Angle N-CA-HA, observed: 123.115, delta from target: -13.115
   A  51  ILE  HA , Angle CB-CA-HA, observed: 94.320, delta from target: 14.680
   A 128  MET  HA , Angle C-CA-HA, observed: 95.223, delta from target: 14.777
   A 125  LYS  HA , Angle N-CA-HA, observed: 125.028, delta from target: -15.028
   A 128  MET  HA , Angle N-CA-HA, observed: 125.316, delta from target: -15.316
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.861, delta from target: 16.139
   A 126  VAL  HA , Angle CB-CA-HA, observed: 91.722, delta from target: 17.278
   A  93  LEU  HA , Angle C-CA-HA, observed: 126.295, delta from target: -17.295
   A  89  TYR  HA , Angle N-CA-HA, observed: 92.672, delta from target: 17.328
   A  90  SER  HA , Angle N-CA-HA, observed: 90.805, delta from target: 19.195
   A  78  ILE  HA , Angle C-CA-HA, observed: 128.443, delta from target: -19.443
   A 125  LYS  HA , Angle CB-CA-HA, observed: 89.043, delta from target: 19.957
   A  74  ASP  HA , Angle C-CA-HA, observed: 88.261, delta from target: 20.739
   A  78  ILE  HB , Angle CA-CB-HB, observed: 81.115, delta from target: 27.885
   A 126  VAL  HA , Angle N-CA-HA, observed: 150.439, delta from target: -40.439
   A  78  ILE  HA , Angle N-CA-HA, observed: 40.829, delta from target: 69.171

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.015   0.200   2242  Z= 0.771
    Angle     :  3.233  69.171   4079  Z= 1.399
    Chirality :  1.195   6.234    176
    Planarity :  0.014   0.085    327
    Dihedral  : 17.704 134.816    769
    Min Nonbonded Distance : 1.342
  
  Molprobity Statistics.
    All-atom Clashscore : 27.95
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  : 11.68 %
      Favored  : 80.29 %
    Rotamer:
      Outliers : 12.90 %
      Allowed  :  3.23 %
      Favored  : 83.87 %
    Cbeta Deviations :  9.09 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 2.29 %
      Twisted Proline : 0.00 %
      Twisted General : 16.79 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.30 (0.60), residues: 137
    helix: -1.83 (0.49), residues: 63
    sheet:  None (None), residues: 0
    loop : -2.57 (0.68), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.029   0.005   HIS A 135 
   PHE   0.115   0.016   PHE A  67 
   TYR   0.138   0.024   TYR A  81 
   ARG   0.038   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.029   0.005   HIS A 135 
   PHE   0.080   0.016   PHE A  67 
   TYR   0.110   0.028   TYR A  81 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   8.03 %
                favored =  80.29 %
  Rotamer outliers      =  12.90 %
  C-beta deviations     =    12
  Clashscore            =  27.95
  RMS(bonds)            =   0.0148
  RMS(angles)           =   3.23
  MolProbity score      =   3.51

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.72    -0.26  1.90e-02  1.87e+02  13.7*sigma
   A 119  LEU  N
   A 119  LEU  CA          1.46     1.67    -0.21  1.90e-02  1.25e+02  11.2*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.71    -0.19  1.80e-02  1.12e+02  10.6*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.65    -0.19  1.90e-02  1.05e+02  10.2*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.64    -0.18  1.90e-02  9.22e+01   9.6*sigma
   A 123  GLU  N
   A 123  GLU  CA          1.46     1.64    -0.18  1.90e-02  8.94e+01   9.5*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.63    -0.17  1.90e-02  7.94e+01   8.9*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.44    -0.11  1.40e-02  6.15e+01   7.8*sigma
   A 118  ASP  CA
   A 118  ASP  C           1.52     1.69    -0.16  2.10e-02  5.86e+01   7.7*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     1.60    -0.14  1.90e-02  5.71e+01   7.6*sigma
   A 122  ILE  CA
   A 122  ILE  CB          1.54     1.73    -0.19  2.70e-02  4.86e+01   7.0*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.43    -0.10  1.40e-02  4.71e+01   6.9*sigma
   A 124  ALA  C
   A 125  LYS  N           1.33     1.42    -0.09  1.40e-02  4.43e+01   6.7*sigma
   A 125  LYS  N
   A 125  LYS  CA          1.46     1.58    -0.12  1.90e-02  4.24e+01   6.5*sigma
   A  93  LEU  N
   A  93  LEU  CA          1.46     1.35     0.11  1.90e-02  3.47e+01   5.9*sigma
   A  92  THR  CA
   A  92  THR  C           1.52     1.40     0.12  2.10e-02  3.27e+01   5.7*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.54    -0.09  1.60e-02  3.13e+01   5.6*sigma
   A 118  ASP  C
   A 119  LEU  N           1.33     1.40    -0.07  1.40e-02  2.79e+01   5.3*sigma
   A  78  ILE  N
   A  78  ILE  CA          1.46     1.36     0.10  1.90e-02  2.69e+01   5.2*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.55    -0.10  1.90e-02  2.57e+01   5.1*sigma
   A 129  ARG  N
   A 129  ARG  CA          1.46     1.54    -0.08  1.90e-02  1.98e+01   4.4*sigma
   A 126  VAL  CA
   A 126  VAL  CB          1.54     1.65    -0.11  2.70e-02  1.77e+01   4.2*sigma
   A 130  SER  CA
   A 130  SER  C           1.52     1.61    -0.09  2.10e-02  1.69e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.260 (Z= 13.691)
  Mean delta:    0.027 (Z=  1.421)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50    88.54    22.96  1.70e+00  1.82e+02  13.5*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20    89.90    26.30  2.00e+00  1.73e+02  13.1*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   137.22   -25.62  2.00e+00  1.64e+02  12.8*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   141.07   -19.37  1.80e+00  1.16e+02  10.8*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    84.77    26.23  2.80e+00  8.78e+01   9.4*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   137.45   -15.75  1.80e+00  7.65e+01   8.7*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   137.23   -15.53  1.80e+00  7.44e+01   8.6*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   128.41   -16.81  2.00e+00  7.06e+01   8.4*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   136.69   -14.99  1.80e+00  6.94e+01   8.3*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   106.73    14.97  1.80e+00  6.92e+01   8.3*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   107.80    13.90  1.80e+00  5.97e+01   7.7*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.20   -11.30  1.50e+00  5.68e+01   7.5*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   130.72   -14.52  2.00e+00  5.27e+01   7.3*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   122.80   -12.30  1.70e+00  5.23e+01   7.2*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.47   -12.77  1.80e+00  5.03e+01   7.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   102.39    13.81  2.00e+00  4.77e+01   6.9*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    92.37    18.63  2.80e+00  4.43e+01   6.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   102.97    13.23  2.00e+00  4.37e+01   6.6*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   129.43   -18.43  2.80e+00  4.33e+01   6.6*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  C         111.00   128.94   -17.94  2.80e+00  4.10e+01   6.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  78  ILE  O         120.80   109.96    10.84  1.70e+00  4.07e+01   6.4*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N         116.20   103.61    12.59  2.00e+00  3.96e+01   6.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   103.75    12.45  2.00e+00  3.88e+01   6.2*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   124.86   -10.96  1.80e+00  3.71e+01   6.1*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   120.71   -10.31  1.70e+00  3.68e+01   6.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O         120.80   110.56    10.24  1.70e+00  3.63e+01   6.0*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   123.44   -11.84  2.00e+00  3.50e+01   5.9*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   121.28   -11.18  1.90e+00  3.46e+01   5.9*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   121.15   -11.05  1.90e+00  3.38e+01   5.8*sigma
   A  83  THR  CA
   A  83  THR  CB
   A  83  THR  CG2       110.50   120.14    -9.64  1.70e+00  3.22e+01   5.7*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG1       110.40   119.99    -9.59  1.70e+00  3.18e+01   5.6*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   125.35   -11.25  2.00e+00  3.16e+01   5.6*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   120.54   -10.44  1.90e+00  3.02e+01   5.5*sigma
   A 124  ALA  O
   A 124  ALA  C
   A 125  LYS  N         123.00   131.66    -8.66  1.60e+00  2.93e+01   5.4*sigma
   A 116  ASP  N
   A 116  ASP  CA
   A 116  ASP  CB        110.50   119.68    -9.18  1.70e+00  2.91e+01   5.4*sigma
   A 119  LEU  N
   A 119  LEU  CA
   A 119  LEU  CB        110.50   101.36     9.14  1.70e+00  2.89e+01   5.4*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   105.46    10.74  2.00e+00  2.88e+01   5.4*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   131.33    -9.63  1.80e+00  2.86e+01   5.4*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   118.48    -7.98  1.50e+00  2.83e+01   5.3*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80    99.11    11.69  2.20e+00  2.82e+01   5.3*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   102.53     8.97  1.70e+00  2.78e+01   5.3*sigma
   A  92  THR  O
   A  92  THR  C
   A  93  LEU  N         123.00   131.43    -8.43  1.60e+00  2.77e+01   5.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   129.74    -8.94  1.70e+00  2.77e+01   5.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   126.70   -10.50  2.00e+00  2.76e+01   5.3*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   114.64     8.36  1.60e+00  2.73e+01   5.2*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N         116.20   126.56   -10.36  2.00e+00  2.68e+01   5.2*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG1       110.40   101.63     8.77  1.70e+00  2.66e+01   5.2*sigma
   A  15  PHE  CA
   A  15  PHE  CB
   A  15  PHE  CG        113.80   108.73     5.07  1.00e+00  2.57e+01   5.1*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.61    -5.01  1.00e+00  2.51e+01   5.0*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   117.54    -4.94  1.00e+00  2.44e+01   4.9*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O         120.80   129.13    -8.33  1.70e+00  2.40e+01   4.9*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   129.95    -8.25  1.80e+00  2.10e+01   4.6*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   129.92    -8.22  1.80e+00  2.08e+01   4.6*sigma
   A  94  GLY  N
   A  94  GLY  CA
   A  94  GLY  C         113.30   126.35   -13.05  2.90e+00  2.03e+01   4.5*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   129.73    -8.03  1.80e+00  1.99e+01   4.5*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   125.04    -8.84  2.00e+00  1.95e+01   4.4*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   129.63    -7.93  1.80e+00  1.94e+01   4.4*sigma
   A 129  ARG  O
   A 129  ARG  C
   A 130  SER  N         123.00   130.00    -7.00  1.60e+00  1.92e+01   4.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O         120.80   128.07    -7.27  1.70e+00  1.83e+01   4.3*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   124.70    -8.50  2.00e+00  1.81e+01   4.2*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG1       110.40   117.62    -7.22  1.70e+00  1.80e+01   4.2*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.68     5.52  1.30e+00  1.80e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma
   A 132  LEU  N
   A 132  LEU  CA
   A 132  LEU  C         111.00   122.71   -11.71  2.80e+00  1.75e+01   4.2*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   129.13    -7.43  1.80e+00  1.70e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N         116.20   108.00     8.20  2.00e+00  1.68e+01   4.1*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   129.02    -7.32  1.80e+00  1.65e+01   4.1*sigma
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        121.70   128.98    -7.28  1.80e+00  1.64e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   26.299 (Z= 13.505)
  Mean delta:    3.472 (Z=  1.812)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   -67.09  -112.91  5.00e+00  5.10e+02  22.6*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    70.72   109.28  5.00e+00  4.78e+02  21.9*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00    94.09    85.91  5.00e+00  2.95e+02  17.2*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   103.86    76.14  5.00e+00  2.32e+02  15.2*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00  -108.47   -71.53  5.00e+00  2.05e+02  14.3*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -113.11   -66.89  5.00e+00  1.79e+02  13.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00  -113.38   -66.62  5.00e+00  1.78e+02  13.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -114.30   -65.70  5.00e+00  1.73e+02  13.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   116.60    63.40  5.00e+00  1.61e+02  12.7*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   119.72    60.28  5.00e+00  1.45e+02  12.1*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   124.22    55.78  5.00e+00  1.24e+02  11.2*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   126.02    53.98  5.00e+00  1.17e+02  10.8*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   138.93    41.07  5.00e+00  6.75e+01   8.2*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA          0.00    31.29   -31.29  5.00e+00  3.92e+01   6.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -152.11   -27.89  5.00e+00  3.11e+01   5.6*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -152.67   -27.33  5.00e+00  2.99e+01   5.5*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   152.85    27.15  5.00e+00  2.95e+01   5.4*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA          0.00    26.17   -26.17  5.00e+00  2.74e+01   5.2*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   155.05    24.95  5.00e+00  2.49e+01   5.0*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   157.05    22.95  5.00e+00  2.11e+01   4.6*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   159.04    20.96  5.00e+00  1.76e+01   4.2*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00  -159.86   -20.14  5.00e+00  1.62e+01   4.0*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -159.98   -20.02  5.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.002
  Max. delta:  112.907
  Mean delta:   19.831

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.61     6.12  2.00e-01  9.37e+02  30.6*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -3.63     6.07  2.00e-01  9.21e+02  30.3*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.81     5.46  2.00e-01  7.44e+02  27.3*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.51     5.02  2.00e-01  6.31e+02  25.1*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.37     4.88  2.00e-01  5.96e+02  24.4*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.26     3.69  2.00e-01  3.41e+02  18.5*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.85     3.28  2.00e-01  2.69e+02  16.4*sigma
   A 131  ILE  CA
   A 131  ILE  N
   A 131  ILE  C
   A 131  ILE  CB          2.43    -0.19     2.63  2.00e-01  1.73e+02  13.1*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43     3.97    -1.54  2.00e-01  5.93e+01   7.7*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51     3.44    -0.93  2.00e-01  2.15e+01   4.6*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     1.67     0.84  2.00e-01  1.75e+01   4.2*sigma

  Min. delta:    0.000
  Max. delta:    6.122
  Mean delta:    1.051

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O
   A 126  VAL  N             0.152       0.115      230.99   5.7*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.064       0.113       82.93   5.7*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O
   A 127  ARG  N             0.057       0.099       32.87   4.9*sigma

  Min. delta:    0.000
  Max. delta:    0.152
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  71  ILE  HB , Angle CA-CB-HB, observed: 96.436, delta from target: 12.564
   A 132  LEU  HA , Angle N-CA-HA, observed: 97.049, delta from target: 12.951
   A 130  SER  HA , Angle N-CA-HA, observed: 96.331, delta from target: 13.669
   A 130  SER  HA , Angle C-CA-HA, observed: 95.311, delta from target: 13.689
   A 130  SER  HA , Angle CB-CA-HA, observed: 123.947, delta from target: -14.947
   A 128  MET  HA , Angle N-CA-HA, observed: 125.792, delta from target: -15.792
   A 131  ILE  HA , Angle N-CA-HA, observed: 126.801, delta from target: -16.801
   A 122  ILE  HA , Angle N-CA-HA, observed: 128.180, delta from target: -18.180
   A  51  ILE  HA , Angle C-CA-HA, observed: 90.120, delta from target: 18.880
   A 131  ILE  HA , Angle CB-CA-HA, observed: 128.832, delta from target: -19.832
   A  51  ILE  HA , Angle CB-CA-HA, observed: 87.608, delta from target: 21.392
   A  78  ILE  HA , Angle C-CA-HA, observed: 86.942, delta from target: 22.058
   A  78  ILE  HA , Angle CB-CA-HA, observed: 84.766, delta from target: 24.234
   A  78  ILE  HA , Angle N-CA-HA, observed: 134.351, delta from target: -24.351
   A 131  ILE  HA , Angle C-CA-HA, observed: 14.509, delta from target: 94.491

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.019   0.260   2242  Z= 1.012
    Angle     :  3.285  94.491   4079  Z= 1.390
    Chirality :  1.051   6.122    176
    Planarity :  0.015   0.152    327
    Dihedral  : 15.863 112.907    769
    Min Nonbonded Distance : 1.520
  
  Molprobity Statistics.
    All-atom Clashscore : 28.85
    Ramachandran Plot:
      Outliers : 15.33 %
      Allowed  : 11.68 %
      Favored  : 72.99 %
    Rotamer:
      Outliers :  8.87 %
      Allowed  :  6.45 %
      Favored  : 84.68 %
    Cbeta Deviations : 12.88 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 9.92 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.48 (0.64), residues: 137
    helix: -2.61 (0.48), residues: 62
    sheet:  None (None), residues: 0
    loop : -3.42 (0.75), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A  43 
   PHE   0.140   0.023   PHE A  15 
   TYR   0.168   0.021   TYR A  91 
   ARG   0.071   0.013   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A  43 
   PHE   0.096   0.024   PHE A  15 
   TYR   0.117   0.022   TYR A  89 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ILE A  77 "
        model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CB  ASP A  88 "
        model="   2" pdb=" CB  LYS A 125 "
        model="   2" pdb=" CB  VAL A 126 "
        model="   2" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  250

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  PRO A  52 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CB  LYS A  79 "
        model="   4" pdb=" CB  TYR A  89 "
        model="   4" pdb=" CB  THR A  92 "
        model="   4" pdb=" CB  LEU A  93 "
        model="   4" pdb=" CB  ALA A 124 "
        model="   4" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  246

  Time building geometry restraints manager: 0.87 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =  15.33 %
                favored =  72.99 %
  Rotamer outliers      =   8.87 %
  C-beta deviations     =    17
  Clashscore            =  28.85
  RMS(bonds)            =   0.0192
  RMS(angles)           =   3.28
  MolProbity score      =   3.48

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.489, 46.55, 53.076, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 112
        1.23 -     1.43: 365
        1.43 -     1.63: 655
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   4" pdb=" N   LYS A  79 "
       model="   4" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.605 -0.147 1.90e-02 2.77e+03 6.02e+01
  bond model="   4" pdb=" N   LYS A 125 "
       model="   4" pdb=" CA  LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.562 -0.104 1.90e-02 2.77e+03 3.01e+01
  bond model="   4" pdb=" N   SER A 130 "
       model="   4" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.555 -0.097 1.90e-02 2.77e+03 2.60e+01
  bond model="   4" pdb=" CA  ILE A  78 "
       model="   4" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.625 -0.100 2.10e-02 2.27e+03 2.29e+01
  bond model="   4" pdb=" CA  MET A 128 "
       model="   4" pdb=" CB  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.530  1.616 -0.086 2.00e-02 2.50e+03 1.86e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       64.09 -    81.30: 3
       81.30 -    98.51: 17
       98.51 -   115.72: 2945
      115.72 -   132.93: 1104
      132.93 -   150.13: 10
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   4" pdb=" C   TYR A  81 "
        model="   4" pdb=" CA  TYR A  81 "
        model="   4" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     109.00   64.09   44.91 3.00e+00 1.11e-01 2.24e+02
  angle model="   4" pdb=" N   MET A 128 "
        model="   4" pdb=" CA  MET A 128 "
        model="   4" pdb=" CB  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.50   85.67   24.83 1.70e+00 3.46e-01 2.13e+02
  angle model="   4" pdb=" CB  MET A 128 "
        model="   4" pdb=" CA  MET A 128 "
        model="   4" pdb=" HA  MET A 128 "
      ideal   model   delta    sigma   weight residual
     109.00  150.13  -41.13 3.00e+00 1.11e-01 1.88e+02
  angle model="   4" pdb=" N   LYS A 125 "
        model="   4" pdb=" CA  LYS A 125 "
        model="   4" pdb=" HA  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     110.00   71.33   38.67 3.00e+00 1.11e-01 1.66e+02
  angle model="   4" pdb=" C   MET A 128 "
        model="   4" pdb=" CA  MET A 128 "
        model="   4" pdb=" CB  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.10   87.16   22.94 1.90e+00 2.77e-01 1.46e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.85: 936
       25.85 -    51.69: 51
       51.69 -    77.54: 22
       77.54 -   103.39: 4
      103.39 -   129.23: 2
  Dihedral angle restraints: 1015
    sinusoidal: 562
      harmonic: 453
  Sorted by residual:
  dihedral model="   4" pdb=" CA  LYS A  79 "
           model="   4" pdb=" C   LYS A  79 "
           model="   4" pdb=" N   GLY A  80 "
           model="   4" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   50.77  129.23     0      5.00e+00 4.00e-02 6.68e+02
  dihedral model="   4" pdb=" CA  ARG A 129 "
           model="   4" pdb=" C   ARG A 129 "
           model="   4" pdb=" N   SER A 130 "
           model="   4" pdb=" CA  SER A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   71.40  108.60     0      5.00e+00 4.00e-02 4.72e+02
  dihedral model="   4" pdb=" C   TYR A  81 "
           model="   4" pdb=" N   TYR A  81 "
           model="   4" pdb=" CA  TYR A  81 "
           model="   4" pdb=" CB  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -172.05   49.45     0      2.50e+00 1.60e-01 3.91e+02
  ... (remaining 1012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.131: 163
       1.131 -    2.262: 2
       2.262 -    3.393: 0
       3.393 -    4.524: 4
       4  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 49
        1.23 -     1.43: 427
        1.43 -     1.62: 656
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" CA  LYS A 125 "
       model="   2" pdb=" C   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.525  1.417  0.108 2.10e-02 2.27e+03 2.66e+01
  bond model="   2" pdb=" C   ILE A  78 "
       model="   2" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.400 -0.071 1.40e-02 5.10e+03 2.55e+01
  bond model="   2" pdb=" CA  ASP A  88 "
       model="   2" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.614 -0.089 2.10e-02 2.27e+03 1.80e+01
  bond model="   2" pdb=" C   ASP A  88 "
       model="   2" pdb=" N   TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.329  1.379 -0.050 1.40e-02 5.10e+03 1.30e+01
  bond model="   2" pdb=" N   MET A 128 "
       model="   2" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.523 -0.065 1.90e-02 2.77e+03 1.17e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       75.74 -    88.53: 3
       88.53 -   101.33: 37
      101.33 -   114.12: 2798
      114.12 -   126.91: 1206
      126.91 -   139.70: 35
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" CA  VAL A 126 "
        model="   2" pdb=" CB  VAL A 126 "
        model="   2" pdb=" CG2 VAL A 126 "
      ideal   model   delta    sigma   weight residual
     110.40  135.99  -25.59 1.70e+00 3.46e-01 2.27e+02
  angle model="   2" pdb=" C   VAL A 126 "
        model="   2" pdb=" CA  VAL A 126 "
        model="   2" pdb=" CB  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     111.40  139.70  -28.30 1.90e+00 2.77e-01 2.22e+02
  angle model="   2" pdb=" N   ILE A  78 "
        model="   2" pdb=" CA  ILE A  78 "
        model="   2" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.00   75.74   34.26 3.00e+00 1.11e-01 1.30e+02
  angle model="   2" pdb=" CB  VAL A 126 "
        model="   2" pdb=" CA  VAL A 126 "
        model="   2" pdb=" HA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     109.00   79.01   29.99 3.00e+00 1.11e-01 9.99e+01
  angle model="   2" pdb=" N   VAL A 126 "
        model="   2" pdb=" CA  VAL A 126 "
        model="   2" pdb=" HA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     110.00  136.66  -26.66 3.00e+00 1.11e-01 7.90e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 914
       17.91 -    35.83: 68
       35.83 -    53.74: 27
       53.74 -    71.66: 8
       71.66 -    89.57: 2
  Dihedral angle restraints: 1019
    sinusoidal: 562
      harmonic: 457
  Sorted by residual:
  dihedral model="   2" pdb=" CA  GLY A  80 "
           model="   2" pdb=" C   GLY A  80 "
           model="   2" pdb=" N   TYR A  81 "
           model="   2" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -94.41  -85.59     0      5.00e+00 4.00e-02 2.93e+02
  dihedral model="   2" pdb=" C   ILE A  78 "
           model="   2" pdb=" N   ILE A  78 "
           model="   2" pdb=" CA  ILE A  78 "
           model="   2" pdb=" CB  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -154.68   32.68     0      2.50e+00 1.60e-01 1.71e+02
  dihedral model="   2" pdb=" N   ILE A  78 "
           model="   2" pdb=" C   ILE A  78 "
           model="   2" pdb=" CA  ILE A  78 "
           model="   2" pdb=" CB  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  155.92  -32.52     0      2.50e+00 1.60e-01 1.69e+02
  ... (remaining 1016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.175: 165
       1.175 -    2.349: 2
       2.349 -    3.523: 1
       3.523 -    4.697: 5
       4..524 -    5.654: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CA  LEU A  93 "
            model="   4" pdb=" N   LEU A  93 "
            model="   4" pdb=" C   LEU A  93 "
            model="   4" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.14    5.65 2.00e-01 2.50e+01 7.99e+02
  chirality model="   4" pdb=" CA  THR A  92 "
            model="   4" pdb=" N   THR A  92 "
            model="   4" pdb=" C   THR A  92 "
            model="   4" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.66    5.18 2.00e-01 2.50e+01 6.71e+02
  chirality model="   4" pdb=" CB  ILE A  78 "
            model="   4" pdb=" CA  ILE A  78 "
            model="   4" pdb=" CG1 ILE A  78 "
            model="   4" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.51    5.15 2.00e-01 2.50e+01 6.64e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CA  ARG A 129 "   -0.054 2.00e-02 2.50e+03   1.10e-01 1.21e+02
        model="   4" pdb=" C   ARG A 129 "    0.190 2.00e-02 2.50e+03
        model="   4" pdb=" O   ARG A 129 "   -0.069 2.00e-02 2.50e+03
        model="   4" pdb=" N   SER A 130 "   -0.067 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  91 "   -0.122 2.00e-02 2.50e+03   4.79e-02 6.88e+01
        model="   4" pdb=" CG  TYR A  91 "    0.017 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  91 "    0.025 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  91 "    0.030 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  91 "    0.012 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  91 "    0.007 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  91 "   -0.016 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  91 "   -0.074 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  91 "    0.040 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  91 "    0.054 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  91 "    0.021 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  91 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  12 "    0.094 2.00e-02 2.50e+03   4.34e-02 5.66e+01
        model="   4" pdb=" CG  TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  12 "   -0.024 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  12 "    0.090 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  12 "   -0.045 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  12 "   -0.044 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.29: 432
        2.29 -     2.87: 5146
        2.87 -     3.45: 6081
        3.45 -     4.02: 8001
        4.02 -     4.60: 11810
  Nonbonded interactions: 31470
  Sorted by model distance:
  nonbonded model="   4" pdb=" HA  GLU A 123 "
            model="   4" pdb=" HA  LYS A 125 "
     model   vdw
     1.717 2.440
  nonbonded model="   4" pdb=" O   ASP A   7 "
            model="   4" pdb=" HG  SER A  11 "
     model   vdw
     1.815 1.850
  nonbonded model="   4" pdb=" OE1 GLU A  75 "
            model="   4" pdb=" HH  TYR A  81 "
     model   vdw
     1.829 1.850
  nonbonded model="   4" pdb=" O   LEU A  61 "
            model="   4" pdb=" HG  SER A  65 "
     model   vdw
     1.830 1.850
  nonbonded model="   4" pdb=" H   VAL A 126 "
            model="   4" pdb=" HG2 MET A 128 "
     model   vdw
     1.852 2.270
  ... (remaining 31465 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
697 -    5.871: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CA  LYS A  79 "
            model="   2" pdb=" N   LYS A  79 "
            model="   2" pdb=" C   LYS A  79 "
            model="   2" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.36    5.87 2.00e-01 2.50e+01 8.62e+02
  chirality model="   2" pdb=" CB  ILE A  78 "
            model="   2" pdb=" CA  ILE A  78 "
            model="   2" pdb=" CG1 ILE A  78 "
            model="   2" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.39    5.03 2.00e-01 2.50e+01 6.34e+02
  chirality model="   2" pdb=" CA  HIS A 139 "
            model="   2" pdb=" N   HIS A 139 "
            model="   2" pdb=" C   HIS A 139 "
            model="   2" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.23    4.74 2.00e-01 2.50e+01 5.61e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  50 "    0.255 2.00e-02 2.50e+03   1.01e-01 3.09e+02
        model="   2" pdb=" CG  TYR A  50 "   -0.038 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  50 "   -0.050 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  50 "   -0.064 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  50 "   -0.030 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  50 "    0.026 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  50 "    0.166 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  50 "   -0.072 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  50 "   -0.114 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  50 "   -0.052 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CA  LYS A 125 "    0.046 2.00e-02 2.50e+03   9.62e-02 9.25e+01
        model="   2" pdb=" C   LYS A 125 "   -0.166 2.00e-02 2.50e+03
        model="   2" pdb=" O   LYS A 125 "    0.069 2.00e-02 2.50e+03
        model="   2" pdb=" N   VAL A 126 "    0.051 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  12 "    0.120 2.00e-02 2.50e+03   5.32e-02 8.48e+01
        model="   2" pdb=" CG  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  12 "    0.109 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  12 "   -0.050 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  12 "   -0.029 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  12 "   -0.042 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.40 -     2.04: 54
        2.04 -     2.68: 3243
        2.68 -     3.32: 6719
        3.32 -     3.96: 8031
        3.96 -     4.60: 12110
  Nonbonded interactions: 30157
  Sorted by model distance:
  nonbonded model="   2" pdb=" HA  VAL A 126 "
            model="   2" pdb=" H   ARG A 129 "
     model   vdw
     1.399 2.270
  nonbonded model="   2" pdb=" OD1 ASP A  95 "
            model="   2" pdb=" HG  SER A  97 "
     model   vdw
     1.707 1.850
  nonbonded model="   2" pdb="HD13 ILE A  86 "
            model="   2" pdb=" HB2 LYS A 101 "
     model   vdw
     1.718 2.440
  nonbonded model="   2" pdb="HG13 ILE A  86 "
            model="   2" pdb=" H   TYR A  91 "
     model   vdw
     1.723 2.270
  nonbonded model="   2" pdb=" H   ILE A  77 "
            model="   2" pdb=" HA  ILE A  77 "
     model   vdw
     1.754 1.816
  ... (remaining 30152 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (43.537, 72.971, 35.822, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (64.018, 78.311, 38.715, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  HIS A 138 "
        model="   5" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  258

  Time building geometry restraints manager: 1.23 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.294, 35.805, 52.459, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A LEU  119": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 55
        1.23 -     1.43: 418
        1.43 -     1.62: 659
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" N   GLY A  80 "
       model="   5" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.541 -0.090 1.60e-02 3.91e+03 3.17e+01
  bond model="   5" pdb=" N   SER A  90 "
       model="   5" pdb=" CA  SER A  90 "
    ideal  model  delta    sigma   weight residual
    1.458  1.554 -0.096 1.90e-02 2.77e+03 2.55e+01
  bond model="   5" pdb=" C   ASP A  88 "
       model="   5" pdb=" N   TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.329  1.384 -0.055 1.40e-02 5.10e+03 1.54e+01
  bond model="   5" pdb=" CA  ASP A  88 "
       model="   5" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.607 -0.082 2.10e-02 2.27e+03 1.54e+01
  bond model="   5" pdb=" CA  LYS A  79 "
       model="   5" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.592 -0.067 2.10e-02 2.27e+03 1.02e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       82.23 -    92.47: 2
       92.47 -   102.72: 35
      102.72 -   112.97: 2643
      112.97 -   123.21: 1182
      123.21 -   133.46: 217
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" C   ASP A  74 "
        model="   5" pdb=" CA  ASP A  74 "
        model="   5" pdb=" CB  ASP A  74 "
      ideal   model   delta    sigma   weight residual
     110.10  131.95  -21.85 1.90e+00 2.77e-01 1.32e+02
  angle model="   5" pdb=" C   ASP A  74 "
        model="   5" pdb=" CA  ASP A  74 "
        model="   5" pdb=" HA  ASP A  74 "
      ideal   model   delta    sigma   weight residual
     109.00   82.23   26.77 3.00e+00 1.11e-01 7.97e+01
  angle model="   5" pdb=" CA  ASP A  47 "
        model="   5" pdb=" CB  ASP A  47 "
        model="   5" pdb=" CG  ASP A  47 "
      ideal   model   delta    sigma   weight residual
     112.60  120.65   -8.05 1.00e+00 1.00e+00 6.48e+01
  angle model="   5" pdb=" CA  LYS A  79 "
        model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CG  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     114.10  128.47  -14.37 2.00e+00 2.50e-01 5.16e+01
  angle model="   5" pdb=" C   SER A  90 "
        model="   5" pdb=" N   TYR A  91 "
        model="   5" pdb=" CA  TYR A  91 "
      ideal   model   delta    sigma   weight residual
     121.70  109.54   12.16 1.80e+00 3.09e-01 4.56e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.37: 932
       21.37 -    42.74: 69
       42.74 -    64.10: 18
       64.10 -    85.47: 6
       85.47 -   106.84: 2
  Dihedral angle restraints: 1027
    sinusoidal: 562
      harmonic: 465
  Sorted by residual:
  dihedral model="   5" pdb=" CA  TYR A  89 "
           model="   5" pdb=" C   TYR A  89 "
           model="   5" pdb=" N   SER A  90 "
           model="   5" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -73.16 -106.84     0      5.00e+00 4.00e-02 4.57e+02
  dihedral model="   5" pdb=" CA  SER A  90 "
           model="   5" pdb=" C   SER A  90 "
           model="   5" pdb=" N   TYR A  91 "
           model="   5" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -100.06  -79.94     0      5.00e+00 4.00e-02 2.56e+02
  dihedral model="   5" pdb=" CA  GLY A  80 "
           model="   5" pdb=" C   GLY A  80 "
           model="   5" pdb=" N   TYR A  81 "
           model="   5" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  102.54   77.46     0      5.00e+00 4.00e-02 2.40e+02
  ... (remaining 1024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.950: 170
       0.950 -    1.900: 3
       1.900 -    2.850: 0
       2.850 -    3.800: 0
       3.800 -    4.749: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CA  HIS A 139 "
            model="   5" pdb=" N   HIS A 139 "
            model="   5" pdb=" C   HIS A 139 "
            model="   5" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.24    4.75 2.00e-01 2.50e+01 5.64e+02
  chirality model="   5" pdb=" CA  HIS A 138 "
            model="   5" pdb=" N   HIS A 138 "
            model="   5" pdb=" C   HIS A 138 "
            model="   5" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.20    4.71 2.00e-01 2.50e+01 5.54e+02
  chirality model="   5" pdb=" CA  ILE A  51 "
            model="   5" pdb=" N   ILE A  51 "
            model="   5" pdb=" C   ILE A  51 "
            model="   5" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -1.79    4.22 2.00e-01 2.50e+01 4.45e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  91 "    0.618 2.00e-02 2.50e+03   2.73e-01 2.23e+03
        model="   5" pdb=" CG  TYR A  91 "   -0.030 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  91 "   -0.222 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  91 "   -0.066 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  91 "    0.049 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  91 "   -0.089 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  91 "    0.098 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  91 "    0.269 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  91 "   -0.521 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  91 "   -0.074 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  91 "    0.193 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  91 "   -0.226 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  12 "    0.152 2.00e-02 2.50e+03   6.67e-02 1.33e+02
        model="   5" pdb=" CG  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  12 "   -0.031 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  12 "   -0.032 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  12 "   -0.023 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  12 "    0.136 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  12 "   -0.051 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  12 "   -0.055 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  12 "   -0.041 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  12 "   -0.038 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" C   ILE A  51 "    0.090 5.00e-02 4.00e+02   1.34e-01 2.85e+01
        model="   5" pdb=" N   PRO A  52 "   -0.231 5.00e-02 4.00e+02
        model="   5" pdb=" CA  PRO A  52 "    0.073 5.00e-02 4.00e+02
        model="   5" pdb=" CD  PRO A  52 "    0.068 5.00e-02 4.00e+02
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.28: 354
        2.28 -     2.86: 5106
        2.86 -     3.44: 6080
        3.44 -     4.02: 7862
        4.02 -     4.60: 11655
  Nonbonded interactions: 31057
  Sorted by model distance:
  nonbonded model="   5" pdb=" HG2 LYS A  79 "
            model="   5" pdb=" H   GLY A  80 "
     model   vdw
     1.695 2.270
  nonbonded model="   5" pdb=" H   ILE A  78 "
            model="   5" pdb=" HB  ILE A  78 "
     model   vdw
     1.702 2.270
  nonbonded model="   5" pdb=" HA  TYR A  89 "
            model="   5" pdb=" HB2 SER A  90 "
     model   vdw
     1.742 2.440
  nonbonded model="   5" pdb=" OD1 ASP A  95 "
            model="   5" pdb=" HG  SER A  97 "
     model   vdw
     1.754 1.850
  nonbonded model="   5" pdb=" OD1 ASP A  44 "
            model="   5" pdb=" HG  SER A  46 "
     model   vdw
     1.762 1.850
  ... (remaining 31052 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.56    -0.11  1.90e-02  3.06e+01   5.5*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.54    -0.09  1.60e-02  2.85e+01   5.3*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.55    -0.09  1.90e-02  2.42e+01   4.9*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.37     0.09  1.90e-02  2.23e+01   4.7*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.62    -0.09  2.10e-02  1.97e+01   4.4*sigma

  Min. delta:    0.000 (Z=  0.004)
  Max. delta:    0.105 (Z=  5.534)
  Mean delta:    0.017 (Z=  0.883)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   135.47   -23.87  2.00e+00  1.42e+02  11.9*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   140.06   -18.36  1.80e+00  1.04e+02  10.2*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20    96.58    19.62  2.00e+00  9.63e+01   9.8*sigma
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        121.70   139.05   -17.35  1.80e+00  9.29e+01   9.6*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   125.46   -15.06  1.70e+00  7.84e+01   8.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.64   -11.74  1.50e+00  6.13e+01   7.8*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   134.80   -13.10  1.80e+00  5.30e+01   7.3*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40    97.77    13.63  1.90e+00  5.15e+01   7.2*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   102.29    13.91  2.00e+00  4.84e+01   7.0*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   133.85   -12.15  1.80e+00  4.55e+01   6.7*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   133.71   -12.01  1.80e+00  4.45e+01   6.7*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   122.28   -12.18  1.90e+00  4.11e+01   6.4*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   118.87    -6.27  1.00e+00  3.93e+01   6.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   131.36   -10.56  1.70e+00  3.86e+01   6.2*sigma
   A 122  ILE  C
   A 122  ILE  CA
   A 122  ILE  CB        111.60   123.48   -11.88  2.00e+00  3.53e+01   5.9*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   124.36   -10.46  1.80e+00  3.38e+01   5.8*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.06   -10.36  1.80e+00  3.31e+01   5.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.30    -5.70  1.00e+00  3.25e+01   5.7*sigma
   A  70  LEU  N
   A  70  LEU  CA
   A  70  LEU  CB        110.50   100.81     9.69  1.70e+00  3.25e+01   5.7*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   120.09    -9.69  1.70e+00  3.25e+01   5.7*sigma
   A 126  VAL  O
   A 126  VAL  C
   A 127  ARG  N         123.00   132.06    -9.06  1.60e+00  3.20e+01   5.7*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  CB        110.50   120.00    -9.50  1.70e+00  3.12e+01   5.6*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   102.14     9.36  1.70e+00  3.03e+01   5.5*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   111.90     9.80  1.80e+00  2.96e+01   5.4*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   118.00    -5.40  1.00e+00  2.92e+01   5.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.20    -9.50  1.80e+00  2.78e+01   5.3*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.45    -9.85  2.00e+00  2.42e+01   4.9*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   130.49    -8.79  1.80e+00  2.38e+01   4.9*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   113.06     8.64  1.80e+00  2.30e+01   4.8*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   119.10    -9.00  1.90e+00  2.25e+01   4.7*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   118.39    -7.89  1.70e+00  2.15e+01   4.6*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00   123.94   -12.94  2.80e+00  2.14e+01   4.6*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    98.26    12.74  2.80e+00  2.07e+01   4.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.29     5.91  1.30e+00  2.07e+01   4.5*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   118.66    -8.56  1.90e+00  2.03e+01   4.5*sigma
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        121.70   129.80    -8.10  1.80e+00  2.03e+01   4.5*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   118.60    -8.50  1.90e+00  2.00e+01   4.5*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   129.61    -7.91  1.80e+00  1.93e+01   4.4*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   103.20     7.30  1.70e+00  1.84e+01   4.3*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   124.68    -8.48  2.00e+00  1.80e+01   4.2*sigma
   A  92  THR  O
   A  92  THR  C
   A  93  LEU  N         123.00   129.78    -6.78  1.60e+00  1.79e+01   4.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.61     7.19  1.70e+00  1.79e+01   4.2*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.32    -5.92  1.40e+00  1.79e+01   4.2*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   129.27    -7.57  1.80e+00  1.77e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A 123  GLU  O
   A 123  GLU  C
   A 124  ALA  N         123.00   116.43     6.57  1.60e+00  1.68e+01   4.1*sigma
   A 123  GLU  CA
   A 123  GLU  CB
   A 123  GLU  CG        114.10   122.28    -8.18  2.00e+00  1.67e+01   4.1*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   129.03    -7.33  1.80e+00  1.66e+01   4.1*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.94     5.26  1.30e+00  1.64e+01   4.0*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   117.75    -7.65  1.90e+00  1.62e+01   4.0*sigma
   A  78  ILE  CB
   A  78  ILE  CG1
   A  78  ILE  CD1       113.80   122.23    -8.43  2.10e+00  1.61e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:   23.870 (Z= 11.935)
  Mean delta:    2.969 (Z=  1.602)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   -93.72   -86.28  5.00e+00  2.98e+02  17.3*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -101.07   -78.93  5.00e+00  2.49e+02  15.8*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   104.95    75.05  5.00e+00  2.25e+02  15.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   106.93    73.07  5.00e+00  2.14e+02  14.6*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -110.62   -69.38  5.00e+00  1.93e+02  13.9*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   110.91    69.09  5.00e+00  1.91e+02  13.8*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00  -112.52   -67.48  5.00e+00  1.82e+02  13.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -114.14   -65.86  5.00e+00  1.73e+02  13.2*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   126.70    53.30  5.00e+00  1.14e+02  10.7*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   131.60    48.40  5.00e+00  9.37e+01   9.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00  -134.31   -45.69  5.00e+00  8.35e+01   9.1*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   139.01    40.99  5.00e+00  6.72e+01   8.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   139.58    40.42  5.00e+00  6.54e+01   8.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   143.91    36.09  5.00e+00  5.21e+01   7.2*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -145.18   -34.82  5.00e+00  4.85e+01   7.0*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -145.56   -34.44  5.00e+00  4.75e+01   6.9*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   149.88    30.12  5.00e+00  3.63e+01   6.0*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   150.38    29.62  5.00e+00  3.51e+01   5.9*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -154.13   -25.87  5.00e+00  2.68e+01   5.2*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -156.28   -23.72  5.00e+00  2.25e+01   4.7*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   156.69    23.31  5.00e+00  2.17e+01   4.7*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00   158.35    21.65  5.00e+00  1.88e+01   4.3*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   158.44    21.56  5.00e+00  1.86e+01   4.3*sigma

  Min. delta:    0.015
  Max. delta:   86.277
  Mean delta:   19.472

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.93     5.45  2.00e-01  7.41e+02  27.2*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.53     5.18  2.00e-01  6.71e+02  25.9*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.65     5.09  2.00e-01  6.48e+02  25.5*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.38     5.03  2.00e-01  6.32e+02  25.1*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -2.37     4.88  2.00e-01  5.95e+02  24.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.27     4.82  2.00e-01  5.81e+02  24.1*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.21     4.72  2.00e-01  5.58e+02  23.6*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.20     4.71  2.00e-01  5.54e+02  23.5*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.08     4.59  2.00e-01  5.26e+02  22.9*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.12     4.56  2.00e-01  5.19e+02  22.8*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.07     3.50  2.00e-01  3.07e+02  17.5*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43     0.47     1.96  2.00e-01  9.65e+01   9.8*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51     1.47     1.04  2.00e-01  2.70e+01   5.2*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53     1.65     0.87  2.00e-01  1.90e+01   4.4*sigma

  Min. delta:    0.000
  Max. delta:    5.445
  Mean delta:    1.222

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.065
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    3" pdbres="HIS A  43  conformer  : HE2, HD1 
    3" pdbres="HIS A 134  conformer  : HE2, HD1 
    3" pdbres="HIS A 135  conformer  : HE2, HD1 
    3" pdbres="HIS A 136  conformer  : HE2, HD1 
    3" pdbres="HIS A 137  conformer  : HE2, HD1 
    3" pdbres="HIS A 138  conformer  : HE2, HD1 
    3" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 126  VAL  HB , Angle CA-CB-HB, observed: 96.717, delta from target: 12.283
   A  74  ASP  HA , Angle C-CA-HA, observed: 96.560, delta from target: 12.440
   A  90  SER  HA , Angle N-CA-HA, observed: 97.463, delta from target: 12.537
   A  98  SER  HA , Angle N-CA-HA, observed: 96.019, delta from target: 13.981
   A  78  ILE  HB , Angle CA-CB-HB, observed: 93.656, delta from target: 15.344
   A  51  ILE  HA , Angle CB-CA-HA, observed: 93.483, delta from target: 15.517
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.009, delta from target: 15.991
   A 122  ILE  HA , Angle CB-CA-HA, observed: 92.936, delta from target: 16.064
   A  97  SER  HA , Angle C-CA-HA, observed: 92.713, delta from target: 16.287
   A  92  THR  HA , Angle N-CA-HA, observed: 90.506, delta from target: 19.494
   A  78  ILE  HA , Angle CB-CA-HA, observed: 78.347, delta from target: 30.653
   A  78  ILE  HA , Angle N-CA-HA, observed: 150.251, delta from target: -40.251
   A  78  ILE  HA , Angle C-CA-HA, observed: 68.233, delta from target: 40.767

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.105   2242  Z= 0.629
    Angle     :  2.743  40.767   4079  Z= 1.198
    Chirality :  1.222   5.445    176
    Planarity :  0.012   0.065    327
    Dihedral  : 15.836  86.277    769
    Min Nonbonded Distance : 1.469
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  8.76 %
      Allowed  :  9.49 %
      Favored  : 81.75 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  7.26 %
      Favored  : 85.48 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 12.98 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.60 (0.64), residues: 137
    helix: -1.85 (0.53), residues: 69
    sheet: -6.18 (0.49), residues: 10
    loop : -2.17 (0.80), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A 136 
   PHE   0.095   0.026   PHE A  15 
   TYR   0.144   0.025   TYR A  91 
   ARG   0.020   0.004   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A 136 
   PHE   0.063   0.027   PHE A  15 
   TYR   0.117   0.028   TYR A  91 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A VAL  112": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   8.76 %
                favored =  81.75 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    16
  Clashscore            =  11.27
  RMS(bonds)            =   0.0121
  RMS(angles)           =   2.74
  MolProbity score      =   2.93

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Time building chain proxies: 0.83, per 1000 atoms: 0.37
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.419, 48.102, 50.728, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.466, 48.674, 55.637, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A LEU    2": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 0.74, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.179, 57.788, 55.685, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ILE A  78 "
        model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CB  TYR A  89 "
        model="   2" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 0.91 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.04, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.76, 61.716, 55.665, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 47
        1.23 -     1.42: 427
        1.42 -     1.62: 658
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" N   LYS A  79 "
       model="   2" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.521 -0.063 1.90e-02 2.77e+03 1.12e+01
  bond model="   2" pdb=" C   ILE A  78 "
       model="   2" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.373 -0.044 1.40e-02 5.10e+03 9.72e+00
  bond model="   2" pdb=" C   ILE A  77 "
       model="   2" pdb=" N   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.329  1.286  0.043 1.40e-02 5.10e+03 9.52e+00
  bond model="   2" pdb=" C   THR A  83 "
       model="   2" pdb=" N   GLU A  84 "
    ideal  model  delta    sigma   weight residual
    1.329  1.288  0.041 1.40e-02 5.10e+03 8.53e+00
  bond model="   2" pdb=" CZ  ARG A  21 "
       model="   2" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.10e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       87.82 -    97.12: 6
       97.12 -   106.42: 183
      106.42 -   115.72: 2794
      115.72 -   125.01: 1026
      125.01 -   134.31: 70
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" C   ILE A  51 "
        model="   2" pdb=" CA  ILE A  51 "
        model="   2" pdb=" CB  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     111.60  126.55  -14.95 2.00e+00 2.50e-01 5.59e+01
  angle model="   2" pdb=" C   ILE A  51 "
        model="   2" pdb=" CA  ILE A  51 "
        model="   2" pdb=" HA  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   87.82   21.18 3.00e+00 1.11e-01 4.98e+01
  angle model="   2" pdb=" C   TYR A  89 "
        model="   2" pdb=" CA  TYR A  89 "
        model="   2" pdb=" CB  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.10  123.41  -13.31 1.90e+00 2.77e-01 4.91e+01
  angle model="   2" pdb=" C   ASP A  88 "
        model="   2" pdb=" N   TYR A  89 "
        model="   2" pdb=" CA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     121.70  134.31  -12.61 1.80e+00 3.09e-01 4.91e+01
  angle model="   2" pdb=" C   ILE A  78 "
        model="   2" pdb=" N   LYS A  79 "
        model="   2" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  133.78  -12.08 1.80e+00 3.09e-01 4.51e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 943
       16.85 -    33.71: 51
       33.71 -    50.56: 16
       50.56 -    67.42: 10
       67.42 -    84.27: 3
  Dihedral angle restraints: 1023
    sinusoidal: 562
      harmonic: 461
  Sorted by residual:
  dihedral model="   2" pdb=" CA  TYR A  89 "
           model="   2" pdb=" C   TYR A  89 "
           model="   2" pdb=" N   SER A  90 "
           model="   2" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -110.63  -69.37     0      5.00e+00 4.00e-02 1.92e+02
  dihedral model="   2" pdb=" CA  TYR A  91 "
           model="   2" pdb=" C   TYR A  91 "
           model="   2" pdb=" N   THR A  92 "
           model="   2" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.13   52.87     0      5.00e+00 4.00e-02 1.12e+02
  dihedral model="   2" pdb=" CA  THR A  92 "
           model="   2" pdb=" C   THR A  92 "
           model="   2" pdb=" N   LEU A  93 "
           model="   2" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.90   45.10     0      5.00e+00 4.00e-02 8.14e+01
  ... (remaining 1020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.131: 170
       1.131 -    2.262: 0
       2.262 -    3.393: 0
       3.393 -    4.524: 3
       4.524 -    5.655: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CA  LYS A  79 "
            model="   2" pdb=" N   LYS A  79 "
            model="   2" pdb=" C   LYS A  79 "
            model="   2" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.14    5.65 2.00e-01 2.50e+01 7.99e+02
  chirality model="   2" pdb=" CB  ILE A  78 "
            model="   2" pdb=" CA  ILE A  78 "
            model="   2" pdb=" CG1 ILE A  78 "
            model="   2" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.52    5.17 2.00e-01 2.50e+01 6.68e+02
  chirality model="   2" pdb=" CA  HIS A 139 "
            model="   2" pdb=" N   HIS A 139 "
            model="   2" pdb=" C   HIS A 139 "
            model="   2" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.40    4.91 2.00e-01 2.50e+01 6.02e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  50 "    0.205 2.00e-02 2.50e+03   8.76e-02 2.30e+02
        model="   2" pdb=" CG  TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  50 "   -0.041 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  50 "   -0.045 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  50 "   -0.031 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  50 "    0.174 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  50 "   -0.064 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  50 "   -0.076 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  50 "   -0.049 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  50 "   -0.038 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  PHE A  15 "   -0.218 2.00e-02 2.50e+03   8.42e-02 2.13e+02
        model="   2" pdb=" CG  PHE A  15 "    0.048 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 PHE A  15 "    0.052 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 PHE A  15 "    0.057 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 PHE A  15 "    0.009 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 PHE A  15 "    0.004 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  PHE A  15 "   -0.041 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 PHE A  15 "    0.084 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 PHE A  15 "    0.098 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 PHE A  15 "    0.012 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   2" pdb=" HZ  PHE A  15 "   -0.104 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  91 "    0.176 2.00e-02 2.50e+03   7.58e-02 1.73e+02
        model="   2" pdb=" CG  TYR A  91 "    0.011 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  91 "   -0.027 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  91 "   -0.047 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  91 "   -0.028 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  91 "   -0.006 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  91 "    0.021 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  91 "    0.122 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  91 "   -0.052 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  91 "   -0.111 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  91 "   -0.062 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  91 "    0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.35: 609
        2.35 -     2.91: 5303
        2.91 -     3.47: 5649
        3.47 -     4.04: 7471
        4.04 -     4.60: 11050
  Nonbonded interactions: 30082
  Sorted by model distance:
  nonbonded model="   2" pdb=" OD1 ASP A  95 "
            model="   2" pdb=" HG  SER A  97 "
     model   vdw
     1.782 1.850
  nonbonded model="   2" pdb="HG22 ILE A  86 "
            model="   2" pdb=" HD1 TYR A  89 "
     model   vdw
     1.800 2.270
  nonbonded model="   2" pdb=" HG  SER A  13 "
            model="   2" pdb=" OE1 GLN A  66 "
     model   vdw
     1.827 1.850
  nonbonded model="   2" pdb=" OE2 GLU A  49 "
            model="   2" pdb=" HH  TYR A  50 "
     model   vdw
     1.828 1.850
  nonbonded model="   2" pdb=" O   ASP A   7 "
            model="   2" pdb=" HG  SER A  11 "
     model   vdw
     1.832 1.850
  ... (remaining 30077 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}

  Symmetric amino acids flipped
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CB  ILE A  78 "
        model="   6" pdb=" CB  THR A  92 "
        model="   6" pdb=" CB  SER A  98 "
        model="   6" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.03, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (40.288, 59.157, 69.362, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.841, 51.255, 41.399, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 66
        1.23 -     1.43: 407
        1.43 -     1.62: 659
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   6" pdb=" N   GLY A  80 "
       model="   6" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.574 -0.123 1.60e-02 3.91e+03 5.87e+01
  bond model="   6" pdb=" CA  LYS A  79 "
       model="   6" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.593 -0.068 2.10e-02 2.27e+03 1.06e+01
  bond model="   6" pdb=" CD2 HIS A 139 "
       model="   6" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.78e+00
  bond model="   6" pdb=" CD2 HIS A 136 "
       model="   6" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.47e+00
  bond model="   6" pdb=" C   SER A  97 "
       model="   6" pdb=" N   SER A  98 "
    ideal  model  delta    sigma   weight residual
    1.329  1.291  0.038 1.40e-02 5.10e+03 7.40e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       73.23 -    87.18: 1
       87.18 -   101.13: 18
      101.13 -   115.08: 2939
      115.08 -   129.03: 1109
      129.03 -   142.97: 12
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   6" pdb=" N   TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.00   73.23   36.77 3.00e+00 1.11e-01 1.50e+02
  angle model="   6" pdb=" CB  TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00  142.97  -33.97 3.00e+00 1.11e-01 1.28e+02
  angle model="   6" pdb=" N   TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" C   TYR A  89 "
      ideal   model   delta    sigma   weight residual
     111.00  140.27  -29.27 2.80e+00 1.28e-01 1.09e+02
  angle model="   6" pdb=" C   TYR A  89 "
        model="   6" pdb=" N   SER A  90 "
        model="   6" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  106.69   15.01 1.80e+00 3.09e-01 6.95e+01
  angle model="   6" pdb=" C   ILE A  77 "
        model="   6" pdb=" CA  ILE A  77 "
        model="   6" pdb=" CB  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     111.60  127.99  -16.39 2.00e+00 2.50e-01 6.71e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.04: 960
       24.04 -    48.08: 47
       48.08 -    72.13: 13
       72.13 -    96.17: 2
       96.17 -   120.21: 1
  Dihedral angle restraints: 1023
    sinusoidal: 562
      harmonic: 461
  Sorted by residual:
  dihedral model="   6" pdb=" CA  SER A  90 "
           model="   6" pdb=" C   SER A  90 "
           model="   6" pdb=" N   TYR A  91 "
           model="   6" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -59.79 -120.21     0      5.00e+00 4.00e-02 5.78e+02
  dihedral model="   6" pdb=" CA  TYR A  89 "
           model="   6" pdb=" C   TYR A  89 "
           model="   6" pdb=" N   SER A  90 "
           model="   6" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -101.48  -78.52     0      5.00e+00 4.00e-02 2.47e+02
  dihedral model="   6" pdb=" CA  ILE A  77 "
           model="   6" pdb=" C   ILE A  77 "
           model="   6" pdb=" N   ILE A  78 "
           model="   6" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  112.59   67.41     0      5.00e+00 4.00e-02 1.82e+02
  ... (remaining 1020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.088: 168
       1.088 -    2.177: 1
       2.177 -    3.265: 0
       3.265 -    4.353: 1
       4.353 -    5.441: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CA  SER A  98 "
            model="   6" pdb=" N   SER A  98 "
            model="   6" pdb=" C   SER A  98 "
            model="   6" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.93    5.44 2.00e-01 2.50e+01 7.40e+02
  chirality model="   6" pdb=" CA  THR A  92 "
            model="   6" pdb=" N   THR A  92 "
            model="   6" pdb=" C   THR A  92 "
            model="   6" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.47    5.00 2.00e-01 2.50e+01 6.25e+02
  chirality model="   6" pdb=" CA  HIS A 139 "
            model="   6" pdb=" N   HIS A 139 "
            model="   6" pdb=" C   HIS A 139 "
            model="   6" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.44    4.95 2.00e-01 2.50e+01 6.14e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  12 "   -0.131 2.00e-02 2.50e+03   5.89e-02 1.04e+02
        model="   6" pdb=" CG  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  12 "    0.026 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  12 "    0.026 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  12 "   -0.123 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  12 "    0.045 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  12 "    0.045 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  12 "    0.038 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  12 "    0.038 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  50 "   -0.084 2.00e-02 2.50e+03   3.81e-02 4.36e+01
        model="   6" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  50 "    0.026 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  50 "   -0.063 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  50 "    0.058 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  50 "    0.040 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CA  GLU A  84 "   -0.027 2.00e-02 2.50e+03   5.36e-02 2.87e+01
        model="   6" pdb=" C   GLU A  84 "    0.093 2.00e-02 2.50e+03
        model="   6" pdb=" O   GLU A  84 "   -0.035 2.00e-02 2.50e+03
        model="   6" pdb=" N   LYS A  85 "   -0.031 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 86
        2.11 -     2.73: 3805
        2.73 -     3.36: 6441
        3.36 -     3.98: 7963
        3.98 -     4.60: 12009
  Nonbonded interactions: 30304
  Sorted by model distance:
  nonbonded model="   6" pdb="HG23 THR A  92 "
            model="   6" pdb=" H   LEU A  99 "
     model   vdw
     1.491 2.270
  nonbonded model="   6" pdb=" H   LEU A  93 "
            model="   6" pdb=" HA  SER A  98 "
     model   vdw
     1.582 2.270
  nonbonded model="   6" pdb=" H   SER A  97 "
            model="   6" pdb=" H   SER A  98 "
     model   vdw
     1.750 2.100
  nonbonded model="   6" pdb=" OD1 ASP A  95 "
            model="   6" pdb=" HG  SER A  97 "
     model   vdw
     1.754 1.850
  nonbonded model="   6" pdb=" HA  ILE A  51 "
            model="   6" pdb=" HB  ILE A  51 "
     model   vdw
     1.776 1.952
  ... (remaining 30299 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 3, 'PTRANS': 7, 'TRANS': 128}

  Symmetric amino acids flipped
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CB  LYS A  79 "
        model="   6" pdb=" CB  SER A  97 "
        model="   6" pdb=" CB  GLU A 123 "
        model="   6" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 1.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  12" pdb=" CB  LEU A   2 "
        model="  12" pdb=" CB  TYR A  81 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 0.73 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 128
        1.23 -     1.43: 344
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" CZ  ARG A  58 "
       model="  12" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.24e+00
  bond model="  12" pdb=" CD2 HIS A 139 "
       model="  12" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.99e+00
  bond model="  12" pdb=" CD2 HIS A 134 "
       model="  12" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.68e+00
  bond model="  12" pdb=" CZ  ARG A  21 "
       model="  12" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.46e+00
  bond model="  12" pdb=" CD2 HIS A 135 "
       model="  12" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.93e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       94.81 -   102.18: 18
      102.18 -   109.55: 1841
      109.55 -   116.92: 1168
      116.92 -   124.29: 939
      124.29 -   131.65: 113
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" C   SER A 130 "
        model="  12" pdb=" CA  SER A 130 "
        model="  12" pdb=" CB  SER A 130 "
      ideal   model   delta    sigma   weight residual
     110.10   97.64   12.46 1.90e+00 2.77e-01 4.30e+01
  angle model="  12" pdb=" C   ILE A 131 "
        model="  12" pdb=" N   LEU A 132 "
        model="  12" pdb=" CA  LEU A 132 "
      ideal   model   delta    sigma   weight residual
     121.70  131.65   -9.95 1.80e+00 3.09e-01 3.06e+01
  angle model="  12" pdb=" CB  HIS A 136 "
        model="  12" pdb=" CG  HIS A 136 "
        model="  12" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  124.45    6.75 1.30e+00 5.92e-01 2.70e+01
  angle model="  12" pdb=" C   LEU A   2 "
        model="  12" pdb=" CA  LEU A   2 "
        model="  12" pdb=" HA  LEU A   2 "
      ideal   model   delta    sigma   weight residual
     109.00   94.81   14.19 3.00e+00 1.11e-01 2.24e+01
  angle model="  12" pdb=" OE1 GLN A  66 "
        model="  12" pdb=" CD  GLN A  66 "
        model="  12" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.90    4.70 1.00e+00 1.00e+00 2.21e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.97: 880
       14.97 -    29.95: 97
       29.95 -    44.92: 25
       44.92 -    59.89: 21
       59.89 -    74.87: 6
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  12" pdb=" CA  MET A   1 "
           model="  12" pdb=" C   MET A   1 "
           model="  12" pdb=" N   LEU A   2 "
           model="  12" pdb=" CA  LEU A   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -130.86  -49.14     0      5.00e+00 4.00e-02 9.66e+01
  dihedral model="  12" pdb=" CA  GLY A  80 "
           model="  12" pdb=" C   GLY A  80 "
           model="  12" pdb=" N   TYR A  81 "
           model="  12" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.04   41.96     0      5.00e+00 4.00e-02 7.04e+01
  dihedral model="  12" pdb=" C   ARG A 129 "
           model="  12" pdb=" N   ARG A 129 "
           model="  12" pdb=" CA  ARG A 129 "
           model="  12" pdb=" CB  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.05   17.45     0      2.50e+00 1.60e-01 4.87e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.935: 174
       0.935 -    1.868: 0
       1.868 -    2.802: 0
       2.802 -    3.735: 0
       3.735 -    4.669: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  TYR A  81 "
            model="  12" pdb=" N   TYR A  81 "
            model="  12" pdb=" C   TYR A  81 "
            model="  12" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.16    4.67 2.00e-01 2.50e+01 5.45e+02
  chirality model="  12" pdb=" CA  LEU A   2 "
            model="  12" pdb=" N   LEU A   2 "
            model="  12" pdb=" C   LEU A   2 "
            model="  12" pdb=" CB  LEU A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.77    4.28 2.00e-01 2.50e+01 4.59e+02
  chirality model="  12" pdb=" CA  ARG A 129 "
            model="  12" pdb=" N   ARG A 129 "
            model="  12" pdb=" C   ARG A 129 "
            model="  12" pdb=" CB  ARG A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.83    0.68 2.00e-01 2.50e+01 1.16e+01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A 111 "   -0.515 2.00e-02 2.50e+03   2.38e-01 1.70e+03
        model="  12" pdb=" CG  TYR A 111 "   -0.082 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A 111 "    0.099 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A 111 "    0.102 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A 111 "    0.065 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A 111 "    0.079 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A 111 "   -0.075 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A 111 "   -0.456 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A 111 "    0.241 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A 111 "    0.244 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A 111 "    0.134 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A 111 "    0.164 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  89 "   -0.492 2.00e-02 2.50e+03   1.85e-01 1.02e+03
        model="  12" pdb=" CG  TYR A  89 "    0.069 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  89 "    0.124 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  89 "    0.110 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  89 "    0.014 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  89 "   -0.075 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  89 "   -0.178 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  89 "    0.237 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  89 "    0.202 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  89 "   -0.024 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  89 "    0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  50 "   -0.267 2.00e-02 2.50e+03   1.56e-01 7.31e+02
        model="  12" pdb=" CG  TYR A  50 "   -0.088 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  50 "    0.072 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  50 "    0.032 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  50 "    0.081 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  50 "   -0.067 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  50 "   -0.316 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  50 "    0.202 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  50 "    0.042 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  50 "    0.073 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  50 "    0.220 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 521
        2.32 -     2.89: 5282
        2.89 -     3.46: 5778
        3.46 -     4.03: 7640
        4.03 -     4.60: 11285
  Nonbonded interactions: 30506
  Sorted by model distance:
  nonbonded model="  12" pdb=" HZ1 LYS A  10 "
            model="  12" pdb=" OD1 ASP A  23 "
     model   vdw
     1.749 1.850
  nonbonded model="  12" pdb=" HG3 LYS A 113 "
            model="  12" pdb=" H   MET A 128 "
     model   vdw
     1.791 2.270
  nonbonded model="  12" pdb=" OD2 ASP A  36 "
            model="  12" pdb=" HZ2 LYS A  40 "
     model   vdw
     1.796 1.850
  nonbonded model="  12" pdb=" HB3 MET A 128 "
            model="  12" pdb=" H   ARG A 129 "
     model   vdw
     1.796 2.270
  nonbonded model="  12" pdb=" H   GLU A  49 "
            model="  12" pdb=" HB2 GLU A  49 "
     model   vdw
     1.799 2.270
  ... (remaining 30501 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 53
        1.23 -     1.43: 422
        1.43 -     1.62: 656
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   6" pdb=" CA  ALA A 124 "
       model="   6" pdb=" C   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.525  1.676 -0.151 2.10e-02 2.27e+03 5.20e+01
  bond model="   6" pdb=" N   ARG A 127 "
       model="   6" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.587 -0.129 1.90e-02 2.77e+03 4.57e+01
  bond model="   6" pdb=" N   GLU A 123 "
       model="   6" pdb=" CA  GLU A 123 "
    ideal  model  delta    sigma   weight residual
    1.458  1.351  0.107 1.90e-02 2.77e+03 3.15e+01
  bond model="   6" pdb=" C   GLU A 123 "
       model="   6" pdb=" N   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.329  1.256  0.073 1.40e-02 5.10e+03 2.75e+01
  bond model="   6" pdb=" C   VAL A 126 "
       model="   6" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.271  0.058 1.40e-02 5.10e+03 1.71e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       89.45 -    99.51: 16
       99.51 -   109.56: 1939
      109.56 -   119.61: 1284
      119.61 -   129.67: 828
      129.67 -   139.72: 12
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   6" pdb=" N   ARG A 127 "
        model="   6" pdb=" CA  ARG A 127 "
        model="   6" pdb=" CB  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     110.50  131.87  -21.37 1.70e+00 3.46e-01 1.58e+02
  angle model="   6" pdb=" C   LYS A 125 "
        model="   6" pdb=" N   VAL A 126 "
        model="   6" pdb=" CA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     121.70  139.72  -18.02 1.80e+00 3.09e-01 1.00e+02
  angle model="   6" pdb=" C   ALA A 124 "
        model="   6" pdb=" CA  ALA A 124 "
        model="   6" pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     110.50  124.28  -13.78 1.50e+00 4.44e-01 8.44e+01
  angle model="   6" pdb=" CA  GLU A 123 "
        model="   6" pdb=" C   GLU A 123 "
        model="   6" pdb=" N   ALA A 124 "
      ideal   model   delta    sigma   weight residual
     116.20   99.34   16.86 2.00e+00 2.50e-01 7.10e+01
  angle model="   6" pdb=" CA  ILE A  78 "
        model="   6" pdb=" CB  ILE A  78 "
        model="   6" pdb=" CG2 ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.50  124.66  -14.16 1.70e+00 3.46e-01 6.94e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.95: 962
       25.95 -    51.90: 47
       51.90 -    77.86: 8
       77.86 -   103.81: 3
      103.81 -   129.76: 3
  Dihedral angle restraints: 1023
    sinusoidal: 562
      harmonic: 461
  Sorted by residual:
  dihedral model="   6" pdb=" CA  VAL A 126 "
           model="   6" pdb=" C   VAL A 126 "
           model="   6" pdb=" N   ARG A 127 "
           model="   6" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   50.24  129.76     0      5.00e+00 4.00e-02 6.74e+02
  dihedral model="   6" pdb=" CA  GLU A 123 "
           model="   6" pdb=" C   GLU A 123 "
           model="   6" pdb=" N   ALA A 124 "
           model="   6" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   62.05  117.95     0      5.00e+00 4.00e-02 5.57e+02
  dihedral model="   6" pdb=" CA  LYS A 125 "
           model="   6" pdb=" C   LYS A 125 "
           model="   6" pdb=" N   VAL A 126 "
           model="   6" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   67.73  112.27     0      5.00e+00 4.00e-02 5.04e+02
  ... (remaining 1020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.996: 171
       0.996 -    1.991: 0
       1.991 -    2.986: 0
       2.986 -    3.980: 1
       3.980 -    4.975: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CA  LYS A  79 "
            model="   6" pdb=" N   LYS A  79 "
            model="   6" pdb=" C   LYS A  79 "
            model="   6" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.46    4.97 2.00e-01 2.50e+01 6.19e+02
  chirality model="   6" pdb=" CA  SER A  97 "
            model="   6" pdb=" N   SER A  97 "
            model="   6" pdb=" C   SER A  97 "
            model="   6" pdb=" CB  SER A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.44    4.95 2.00e-01 2.50e+01 6.13e+02
  chirality model="   6" pdb=" CA  GLU A 123 "
            model="   6" pdb=" N   GLU A 123 "
            model="   6" pdb=" C   GLU A 123 "
            model="   6" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.41    4.92 2.00e-01 2.50e+01 6.06e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  89 "   -0.117 2.00e-02 2.50e+03   7.71e-02 1.78e+02
        model="   6" pdb=" CG  TYR A  89 "    0.007 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  89 "    0.051 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  89 "    0.050 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  89 "   -0.022 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  89 "   -0.129 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  89 "   -0.053 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  89 "    0.117 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  89 "    0.134 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  89 "   -0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  91 "    0.132 2.00e-02 2.50e+03   6.38e-02 1.22e+02
        model="   6" pdb=" CG  TYR A  91 "   -0.020 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  91 "   -0.048 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  91 "   -0.036 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  91 "   -0.015 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  91 "    0.105 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  91 "    0.014 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  91 "   -0.098 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  91 "   -0.068 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  91 "    0.044 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  50 "    0.141 2.00e-02 2.50e+03   5.58e-02 9.34e+01
        model="   6" pdb=" CG  TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  50 "   -0.031 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  50 "   -0.032 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  50 "    0.091 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  50 "   -0.052 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  50 "   -0.057 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.34 -     2.00: 40
        2.00 -     2.65: 2853
        2.65 -     3.30: 6715
        3.30 -     3.95: 8079
        3.95 -     4.60: 12215
  Nonbonded interactions: 29902
  Sorted by model distance:
  nonbonded model="   6" pdb=" HA  ALA A 124 "
            model="   6" pdb=" H   VAL A 126 "
     model   vdw
     1.345 2.270
  nonbonded model="   6" pdb=" H   LYS A  79 "
            model="   6" pdb=" HB  THR A  92 "
     model   vdw
     1.598 2.270
  nonbonded model="   6" pdb=" HA  LYS A 125 "
            model="   6" pdb=" H   ARG A 127 "
     model   vdw
     1.599 2.270
  nonbonded model="   6" pdb="HG23 ILE A  78 "
            model="   6" pdb=" H   THR A  92 "
     model   vdw
     1.672 2.270
  nonbonded model="   6" pdb=" HB1 ALA A 124 "
            model="   6" pdb=" HB  VAL A 126 "
     model   vdw
     1.674 2.440
  ... (remaining 29897 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 1.20, per 1000 atoms: 0.54
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.658, 58.45, 36.718, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 74
        1.23 -     1.42: 398
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" CE1 HIS A  43 "
       model="  13" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.85e+00
  bond model="  13" pdb=" CD2 HIS A 134 "
       model="  13" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.57e+00
  bond model="  13" pdb=" ND1 HIS A 139 "
       model="  13" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.04e+00
  bond model="  13" pdb=" CD2 HIS A 138 "
       model="  13" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.89e+00
  bond model="  13" pdb=" CE1 HIS A 135 "
       model="  13" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.85e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.55 -   105.02: 65
      105.02 -   111.49: 2408
      111.49 -   117.96: 632
      117.96 -   124.43: 875
      124.43 -   130.90: 99
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" C   VAL A 112 "
        model="  13" pdb=" N   LYS A 113 "
        model="  13" pdb=" CA  LYS A 113 "
      ideal   model   delta    sigma   weight residual
     121.70  130.90   -9.20 1.80e+00 3.09e-01 2.61e+01
  angle model="  13" pdb=" CB  HIS A  43 "
        model="  13" pdb=" CG  HIS A  43 "
        model="  13" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  124.76    6.44 1.30e+00 5.92e-01 2.45e+01
  angle model="  13" pdb=" CA  HIS A 137 "
        model="  13" pdb=" CB  HIS A 137 "
        model="  13" pdb=" CG  HIS A 137 "
      ideal   model   delta    sigma   weight residual
     113.80  109.00    4.80 1.00e+00 1.00e+00 2.30e+01
  angle model="  13" pdb=" OE1 GLN A  66 "
        model="  13" pdb=" CD  GLN A  66 "
        model="  13" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.82    4.78 1.00e+00 1.00e+00 2.29e+01
  angle model="  13" pdb=" CA  HIS A 138 "
        model="  13" pdb=" CB  HIS A 138 "
        model="  13" pdb=" CG  HIS A 138 "
      ideal   model   delta    sigma   weight residual
     113.80  118.13   -4.33 1.00e+00 1.00e+00 1.88e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 934
       17.77 -    35.53: 60
       35.53 -    53.30: 20
       53.30 -    71.06: 9
       71.06 -    88.83: 10
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  13" pdb=" CA  HIS A 136 "
           model="  13" pdb=" C   HIS A 136 "
           model="  13" pdb=" N   HIS A 137 "
           model="  13" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.13   21.87     0      5.00e+00 4.00e-02 1.91e+01
  dihedral model="  13" pdb=" C   TYR A  89 "
           model="  13" pdb=" N   TYR A  89 "
           model="  13" pdb=" CA  TYR A  89 "
           model="  13" pdb=" CB  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.90   10.30     0      2.50e+00 1.60e-01 1.70e+01
  dihedral model="  13" pdb=" C   ASP A  74 "
           model="  13" pdb=" N   ASP A  74 "
           model="  13" pdb=" CA  ASP A  74 "
           model="  13" pdb=" CB  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.80   10.20     0      2.50e+00 1.60e-01 1.66e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 100
       0.079 -    0.157: 57
       0.157 -    0.235: 13
       0.235 -    0.314: 4
       0.314 -    0.392: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  ASP A  74 "
            model="  13" pdb=" N   ASP A  74 "
            model="  13" pdb=" C   ASP A  74 "
            model="  13" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.84e+00
  chirality model="  13" pdb=" CA  TYR A  89 "
            model="  13" pdb=" N   TYR A  89 "
            model="  13" pdb=" C   TYR A  89 "
            model="  13" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.21e+00
  chirality model="  13" pdb=" CA  LYS A 113 "
            model="  13" pdb=" N   LYS A 113 "
            model="  13" pdb=" C   LYS A 113 "
            model="  13" pdb=" CB  LYS A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.44e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  89 "    0.212 2.00e-02 2.50e+03   1.40e-01 5.90e+02
        model="  13" pdb=" CG  TYR A  89 "    0.102 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  89 "   -0.066 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  89 "   -0.059 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  89 "    0.141 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  89 "    0.207 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  89 "   -0.033 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  89 "   -0.227 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  89 "   -0.235 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  89 "   -0.044 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  81 "    0.191 2.00e-02 2.50e+03   9.49e-02 2.70e+02
        model="  13" pdb=" CG  TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  81 "   -0.066 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  81 "   -0.013 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  81 "   -0.052 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  81 "    0.020 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  81 "    0.163 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  81 "   -0.145 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  81 "    0.029 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  81 "   -0.125 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  HIS A 135 "    0.146 2.00e-02 2.50e+03   8.91e-02 1.59e+02
        model="  13" pdb=" CG  HIS A 135 "   -0.092 2.00e-02 2.50e+03
        model="  13" pdb=" ND1 HIS A 135 "   -0.144 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 HIS A 135 "   -0.023 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 HIS A 135 "    0.011 2.00e-02 2.50e+03
        model="  13" pdb=" NE2 HIS A 135 "    0.079 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 HIS A 135 "   -0.042 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 HIS A 135 "    0.065 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 433
        2.30 -     2.88: 5231
        2.88 -     3.45: 5858
        3.45 -     4.03: 7500
        4.03 -     4.60: 11541
  Nonbonded interactions: 30563
  Sorted by model distance:
  nonbonded model="  13" pdb=" OD1 ASP A  74 "
            model="  13" pdb=" HG  SER A  76 "
     model   vdw
     1.727 1.850
  nonbonded model="  13" pdb=" HZ1 LYS A  10 "
            model="  13" pdb=" OD1 ASP A  23 "
     model   vdw
     1.745 1.850
  nonbonded model="  13" pdb=" OD2 ASP A  44 "
            model="  13" pdb=" HG  SER A  46 "
     model   vdw
     1.761 1.850
  nonbonded model="  13" pdb="HG22 ILE A  71 "
            model="  13" pdb="HG22 THR A  83 "
     model   vdw
     1.793 2.440
  nonbonded model="  13" pdb=" HG  SER A  17 "
            model="  13" pdb=" OE2 GLU A  75 "
     model   vdw
     1.808 1.850
  ... (remaining 30558 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 0.58, per 1000 atoms: 0.26
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (60.207, 39.112, 51.152, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 129}
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.168, 60.648, 45.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 129}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.727, 42.381, 61.935, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (64.446, 49.195, 66.647, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CB  ILE A  78 "
        model="   3" pdb=" CB  LYS A  79 "
        model="   3" pdb=" CB  TYR A  91 "
        model="   3" pdb=" CB  LEU A  93 "
        model="   3" pdb=" CB  GLU A 123 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.44, 53.874, 76.403, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 52
        1.23 -     1.43: 423
        1.43 -     1.62: 657
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   3" pdb=" N   GLY A  80 "
       model="   3" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.531 -0.080 1.60e-02 3.91e+03 2.48e+01
  bond model="   3" pdb=" CA  ILE A  78 "
       model="   3" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.615 -0.090 2.10e-02 2.27e+03 1.86e+01
  bond model="   3" pdb=" N   ARG A 127 "
       model="   3" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.381  0.077 1.90e-02 2.77e+03 1.65e+01
  bond model="   3" pdb=" CA  ASP A  88 "
       model="   3" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.607 -0.082 2.10e-02 2.27e+03 1.53e+01
  bond model="   3" pdb=" CA  LYS A  79 "
       model="   3" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.606 -0.081 2.10e-02 2.27e+03 1.49e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       86.61 -    96.05: 5
       96.05 -   105.49: 139
      105.49 -   114.93: 2777
      114.93 -   124.37: 1030
      124.37 -   133.81: 128
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   3" pdb=" C   ALA A 124 "
        model="   3" pdb=" CA  ALA A 124 "
        model="   3" pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     110.50  129.30  -18.80 1.50e+00 4.44e-01 1.57e+02
  angle model="   3" pdb=" CA  ILE A  51 "
        model="   3" pdb=" C   ILE A  51 "
        model="   3" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  128.49  -11.59 1.50e+00 4.44e-01 5.97e+01
  angle model="   3" pdb=" CB  ALA A 124 "
        model="   3" pdb=" CA  ALA A 124 "
        model="   3" pdb=" HA  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     109.00   86.61   22.39 3.00e+00 1.11e-01 5.57e+01
  angle model="   3" pdb=" C   TYR A  89 "
        model="   3" pdb=" N   SER A  90 "
        model="   3" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  109.44   12.26 1.80e+00 3.09e-01 4.64e+01
  angle model="   3" pdb=" CA  LYS A  79 "
        model="   3" pdb=" C   LYS A  79 "
        model="   3" pdb=" N   GLY A  80 "
      ideal   model   delta    sigma   weight residual
     116.20  129.47  -13.27 2.00e+00 2.50e-01 4.40e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.87: 944
       21.87 -    43.75: 58
       43.75 -    65.62: 13
       65.62 -    87.49: 5
       87.49 -   109.36: 1
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   3" pdb=" CA  ALA A 124 "
           model="   3" pdb=" C   ALA A 124 "
           model="   3" pdb=" N   LYS A 125 "
           model="   3" pdb=" CA  LYS A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   70.64  109.36     0      5.00e+00 4.00e-02 4.78e+02
  dihedral model="   3" pdb=" CA  THR A  92 "
           model="   3" pdb=" C   THR A  92 "
           model="   3" pdb=" N   LEU A  93 "
           model="   3" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  103.45   76.55     0      5.00e+00 4.00e-02 2.34e+02
  dihedral model="   3" pdb=" CA  SER A 130 "
           model="   3" pdb=" C   SER A 130 "
           model="   3" pdb=" N   ILE A 131 "
           model="   3" pdb=" CA  ILE A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -105.34  -74.66     0      5.00e+00 4.00e-02 2.23e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.179: 167
       1.179 -    2.358: 0
       2.358 -    3.538: 1
       3.538 -    4.717: 0
       4.717 -    5.896: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   3" pdb=" CA  LYS A  79 "
            model="   3" pdb=" N   LYS A  79 "
            model="   3" pdb=" C   LYS A  79 "
            model="   3" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.39    5.90 2.00e-01 2.50e+01 8.69e+02
  chirality model="   3" pdb=" CA  LEU A  93 "
            model="   3" pdb=" N   LEU A  93 "
            model="   3" pdb=" C   LEU A  93 "
            model="   3" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.93    5.44 2.00e-01 2.50e+01 7.40e+02
  chirality model="   3" pdb=" CB  ILE A 122 "
            model="   3" pdb=" CA  ILE A 122 "
            model="   3" pdb=" CG1 ILE A 122 "
            model="   3" pdb=" CG2 ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.67    5.32 2.00e-01 2.50e+01 7.06e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  89 "   -0.288 2.00e-02 2.50e+03   1.13e-01 3.80e+02
        model="   3" pdb=" CG  TYR A  89 "    0.046 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  89 "    0.061 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  89 "    0.069 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  89 "    0.026 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  89 "    0.021 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  89 "   -0.028 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  89 "   -0.179 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  89 "    0.094 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  89 "    0.117 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  89 "    0.038 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  89 "    0.022 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  12 "    0.097 2.00e-02 2.50e+03   4.31e-02 5.58e+01
        model="   3" pdb=" CG  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  12 "   -0.024 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  12 "    0.088 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  12 "   -0.043 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  12 "   -0.036 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  50 "    0.106 2.00e-02 2.50e+03   4.06e-02 4.94e+01
        model="   3" pdb=" CG  TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  50 "    0.058 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  50 "   -0.045 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  50 "   -0.032 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 226
        2.22 -     2.82: 4584
        2.82 -     3.41: 6278
        3.41 -     4.01: 7744
        4.01 -     4.60: 11713
  Nonbonded interactions: 30545
  Sorted by model distance:
  nonbonded model="   3" pdb=" HB  THR A  92 "
            model="   3" pdb=" HB2 LEU A  99 "
     model   vdw
     1.627 2.440
  nonbonded model="   3" pdb=" H   LEU A  93 "
            model="   3" pdb=" HA  SER A  97 "
     model   vdw
     1.671 2.270
  nonbonded model="   3" pdb=" HA  ILE A  71 "
            model="   3" pdb="HG21 ILE A  77 "
     model   vdw
     1.723 2.440
  nonbonded model="   3" pdb=" HA  ILE A  51 "
            model="   3" pdb=" HB  ILE A  51 "
     model   vdw
     1.734 1.952
  nonbonded model="   3" pdb="HG23 ILE A  77 "
            model="   3" pdb="HG21 THR A  92 "
     model   vdw
     1.791 2.440
  ... (remaining 30540 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.06, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.469, 52.542, 45.391, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.13, 54.3, 50.172, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   61": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A VAL  112": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   0" pdb=" CB  ILE A  51 "
        model="   0" pdb=" CB  ILE A  78 "
        model="   0" pdb=" CB  LYS A  79 "
        model="   0" pdb=" CB  TYR A  89 "
        model="   0" pdb=" CB  THR A  92 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CB  ILE A  78 "
        model="   3" pdb=" CB  LYS A  79 "
        model="   3" pdb=" CB  ARG A 127 "
        model="   3" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 1.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.01 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 62
        1.23 -     1.43: 414
        1.43 -     1.62: 654
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" N   LYS A  79 "
       model="   0" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.553 -0.095 1.90e-02 2.77e+03 2.50e+01
  bond model="   0" pdb=" CA  LYS A  79 "
       model="   0" pdb=" CB  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.530  1.622 -0.092 2.00e-02 2.50e+03 2.14e+01
  bond model="   0" pdb=" N   ILE A  77 "
       model="   0" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.545 -0.087 1.90e-02 2.77e+03 2.10e+01
  bond model="   0" pdb=" N   LEU A  93 "
       model="   0" pdb=" CA  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.458  1.377  0.081 1.90e-02 2.77e+03 1.81e+01
  bond model="   0" pdb=" CA  THR A  92 "
       model="   0" pdb=" C   THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.525  1.437  0.088 2.10e-02 2.27e+03 1.77e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       84.54 -    94.48: 4
       94.48 -   104.43: 69
      104.43 -   114.37: 2822
      114.37 -   124.32: 1059
      124.32 -   134.26: 125
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
        model="   0" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.10   84.54   25.56 1.90e+00 2.77e-01 1.81e+02
  angle model="   0" pdb=" N   TYR A  81 "
        model="   0" pdb=" CA  TYR A  81 "
        model="   0" pdb=" CB  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     110.50   95.50   15.00 1.70e+00 3.46e-01 7.78e+01
  angle model="   0" pdb=" CA  THR A  92 "
        model="   0" pdb=" C   THR A  92 "
        model="   0" pdb=" N   LEU A  93 "
      ideal   model   delta    sigma   weight residual
     116.20   98.61   17.59 2.00e+00 2.50e-01 7.73e+01
  angle model="   0" pdb=" CB  LYS A  79 "
        model="   0" pdb=" CG  LYS A  79 "
        model="   0" pdb=" CD  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     111.30  130.37  -19.07 2.30e+00 1.89e-01 6.88e+01
  angle model="   0" pdb=" C   TYR A  89 "
        model="   0" pdb=" CA  TYR A  89 "
        model="   0" pdb=" CB  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.10  125.05  -14.95 1.90e+00 2.77e-01 6.19e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.07: 957
       22.07 -    44.14: 42
       44.14 -    66.21: 19
       66.21 -    88.29: 2
       88.29 -   110.36: 3
  Dihedral angle restraints: 1023
    sinusoidal: 562
      harmonic: 461
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  91 "
           model="   0" pdb=" C   TYR A  91 "
           model="   0" pdb=" N   THR A  92 "
           model="   0" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   69.64  110.36     0      5.00e+00 4.00e-02 4.87e+02
  dihedral model="   0" pdb=" CA  ILE A  77 "
           model="   0" pdb=" C   ILE A  77 "
           model="   0" pdb=" N   ILE A  78 "
           model="   0" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -75.37 -104.63     0      5.00e+00 4.00e-02 4.38e+02
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -82.34  -97.66     0      5.00e+00 4.00e-02 3.81e+02
  ... (remaining 1020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    1.118: 168
       1.118 -    2.235: 0
       2.235 -    3.352: 0
       3.352 -    4.469: 2
       4  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 63
        1.23 -     1.43: 413
        1.43 -     1.62: 656
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   3" pdb=" N   LYS A  79 "
       model="   3" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.588 -0.130 1.90e-02 2.77e+03 4.70e+01
  bond model="   3" pdb=" N   GLY A  80 "
       model="   3" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.560 -0.109 1.60e-02 3.91e+03 4.61e+01
  bond model="   3" pdb=" CA  THR A  92 "
       model="   3" pdb=" C   THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.525  1.415  0.110 2.10e-02 2.27e+03 2.73e+01
  bond model="   3" pdb=" N   MET A 128 "
       model="   3" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.531 -0.073 1.90e-02 2.77e+03 1.49e+01
  bond model="   3" pdb=" N   SER A 130 "
       model="   3" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.531 -0.073 1.90e-02 2.77e+03 1.49e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       80.38 -    92.68: 3
       92.68 -   104.97: 119
      104.97 -   117.26: 2927
      117.26 -   129.56: 1018
      129.56 -   141.85: 12
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   3" pdb=" C   ILE A  78 "
        model="   3" pdb=" N   LYS A  79 "
        model="   3" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  141.85  -20.15 1.80e+00 3.09e-01 1.25e+02
  angle model="   3" pdb=" CD2 LEU A  93 "
        model="   3" pdb=" CG  LEU A  93 "
        model="   3" pdb=" HG  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     108.00   80.38   27.62 3.00e+00 1.11e-01 8.47e+01
  angle model="   3" pdb=" CD1 LEU A  93 "
        model="   3" pdb=" CG  LEU A  93 "
        model="   3" pdb=" CD2 LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.80  127.54  -16.74 2.20e+00 2.07e-01 5.79e+01
  angle model="   3" pdb=" C   LYS A  79 "
        model="   3" pdb=" N   GLY A  80 "
        model="   3" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  135.11  -13.41 1.80e+00 3.09e-01 5.55e+01
  angle model="   3" pdb=" CA  ILE A  51 "
        model="   3" pdb=" C   ILE A  51 "
        model="   3" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  127.72  -10.82 1.50e+00 4.44e-01 5.20e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.99: 958
       24.99 -    49.97: 43
       49.97 -    74.96: 18
       74.96 -    99.95: 1
       99.95 -   124.94: 3
  Dihedral angle restraints: 1023
    sinusoidal: 562
      harmonic: 461
  Sorted by residual:
  dihedral model="   3" pdb=" CA  TYR A  89 "
           model="   3" pdb=" C   TYR A  89 "
           model="   3" pdb=" N   SER A  90 "
           model="   3" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -55.06 -124.94     0      5.00e+00 4.00e-02 6.24e+02
  dihedral model="   3" pdb=" CA  VAL A 126 "
           model="   3" pdb=" C   VAL A 126 "
           model="   3" pdb=" N   ARG A 127 "
           model="   3" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   58.46  121.54     0      5.00e+00 4.00e-02 5.91e+02
  dihedral model="   3" pdb=" CA  THR A  92 "
           model="   3" pdb=" C   THR A  92 "
           model="   3" pdb=" N   LEU A  93 "
           model="   3" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   66.51  113.49     0      5.00e+00 4.00e-02 5.15e+02
  ... (remaining 1020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.133: 167
       1.133 -    2.264: 1
       2.264 -    3.396: 1
       3.396 -    4.527: 1
       4.527 -    5.659: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   3" pdb=" CA  MET A 128 "
            model="   3" pdb=" N   MET A 128 "
            model="   3" pdb=" C   MET A 128 "
            model="   3" pdb=" CB  MET A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.15    5.66 2.00e-01 2.50e+01 8.00e+02
  chirality model="   3" pdb=" CA  LYS A  79 "
            model="   3" pdb=" N   LYS A  79 "
            model="   3" pdb=" C   LYS A  79 "
            model="   3" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.11    5.62 2.00e-01 2.50e+01 7.90e+02
  chirality model="   3" pdb=" CA  ARG A 127 "
            model="   3" pdb=" N   ARG A 127 "
            model="   3" pdb=" C   ARG A 127 "
            model="   3" pdb=" CB  ARG A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.82    5.33 2.00e-01 2.50e+01 7.11e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  91 "   -0.159 2.00e-02 2.50e+03   6.05e-02 1.10e+02
        model="   3" pdb=" CG  TYR A  91 "    0.030 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  91 "    0.037 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  91 "    0.040 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  91 "   -0.042 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  91 "   -0.060 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  91 "    0.064 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  91 "    0.074 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  91 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  50 "    0.135 2.00e-02 2.50e+03   5.10e-02 7.80e+01
        model="   3" pdb=" CG  TYR A  50 "   -0.030 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  50 "   -0.032 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  50 "   -0.032 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  50 "    0.071 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  50 "   -0.050 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  50 "   -0.049 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  50 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A 111 "    0.092 2.00e-02 2.50e+03   3.73e-02 4.17e+01
        model="   3" pdb=" CG  TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A 111 "    0.068 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A 111 "   -0.030 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A 111 "   -0.029 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.16 -     1.85: 12
        1.85 -     2.54: 1813
 .469 -    5.586: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  79 "
            model="   0" pdb=" N   LYS A  79 "
            model="   0" pdb=" C   LYS A  79 "
            model="   0" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.08    5.59 2.00e-01 2.50e+01 7.80e+02
  chirality model="   0" pdb=" CB  ILE A  78 "
            model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" CG1 ILE A  78 "
            model="   0" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.43    5.07 2.00e-01 2.50e+01 6.43e+02
  chirality model="   0" pdb=" CB  THR A  92 "
            model="   0" pdb=" CA  THR A  92 "
            model="   0" pdb=" OG1 THR A  92 "
            model="   0" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.39    4.94 2.00e-01 2.50e+01 6.10e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.379 2.00e-02 2.50e+03   1.69e-01 8.61e+02
        model="   0" pdb=" CG  TYR A  91 "    0.096 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.063 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.103 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.069 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.188 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.192 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.305 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.029 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  THR A  92 "    0.042 2.00e-02 2.50e+03   8.71e-02 7.59e+01
        model="   0" pdb=" C   THR A  92 "   -0.150 2.00e-02 2.50e+03
        model="   0" pdb=" O   THR A  92 "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" N   LEU A  93 "    0.046 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.118 2.00e-02 2.50e+03   4.44e-02 5.92e+01
        model="   0" pdb=" CG  TYR A  50 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.09: 77
        2.09 -     2.72: 3669
        2.72 -     3.35: 6559
        3.35 -     3.97: 7952
        3.97 -     4.60: 12048
  Nonbonded interactions: 30305
  Sorted by model distance:
  nonbonded model="   0" pdb=" HA  ILE A  77 "
            model="   0" pdb=" HB2 LYS A  79 "
     model   vdw
     1.466 2.440
  nonbonded model="   0" pdb=" HG3 LYS A  79 "
            model="   0" pdb=" HA2 GLY A  80 "
     model   vdw
     1.711 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.759 1.850
  nonbonded model="   0" pdb=" H   SER A  90 "
            model="   0" pdb=" HB2 TYR A  91 "
     model   vdw
     1.777 2.270
  nonbonded model="   0" pdb=" HA  TYR A  91 "
            model="   0" pdb=" HA  LEU A  99 "
     model   vdw
     1.781 2.440
  ... (remaining 30300 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
       2.54 -     3.22: 7092
        3.22 -     3.91: 8626
        3.91 -     4.60: 13008
  Nonbonded interactions: 30551
  Sorted by model distance:
  nonbonded model="   3" pdb=" H   GLY A  94 "
            model="   3" pdb=" H   SER A  98 "
     model   vdw
     1.158 2.100
  nonbonded model="   3" pdb=" H   ASP A  95 "
            model="   3" pdb=" H   SER A  97 "
     model   vdw
     1.566 2.100
  nonbonded model="   3" pdb=" HA  MET A 128 "
            model="   3" pdb=" HA  SER A 130 "
     model   vdw
     1.654 2.440
  nonbonded model="   3" pdb=" HA  THR A  92 "
            model="   3" pdb=" HG  LEU A  93 "
     model   vdw
     1.700 2.440
  nonbonded model="   3" pdb=" HA  THR A  92 "
            model="   3" pdb="HD23 LEU A  93 "
     model   vdw
     1.740 2.440
  ... (remaining 30546 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 124
        1.23 -     1.43: 350
        1.43 -     1.63: 657
        1.63 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" CA  ARG A 127 "
       model="  11" pdb=" CB  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.530  1.628 -0.098 2.00e-02 2.50e+03 2.41e+01
  bond model="  11" pdb=" CA  ARG A 129 "
       model="  11" pdb=" CB  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.530  1.605 -0.075 2.00e-02 2.50e+03 1.42e+01
  bond model="  11" pdb=" C   MET A 128 "
       model="  11" pdb=" O   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.231  1.162  0.069 2.00e-02 2.50e+03 1.18e+01
  bond model="  11" pdb=" C   ARG A 127 "
       model="  11" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.284  0.045 1.40e-02 5.10e+03 1.02e+01
  bond model="  11" pdb=" N   PRO A  52 "
       model="  11" pdb=" CA  PRO A  52 "
    ideal  model  delta    sigma   weight residual
    1.466  1.511 -0.045 1.50e-02 4.44e+03 8.98e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       93.89 -   102.49: 18
      102.49 -   111.09: 2366
      111.09 -   119.69: 901
      119.69 -   128.29: 788
      128.29 -   136.88: 6
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" CA  ASP A 116 "
        model="  11" pdb=" CB  ASP A 116 "
        model="  11" pdb=" CG  ASP A 116 "
      ideal   model   delta    sigma   weight residual
     112.60  123.11  -10.51 1.00e+00 1.00e+00 1.10e+02
  angle model="  11" pdb=" CA  ASP A 116 "
        model="  11" pdb=" C   ASP A 116 "
        model="  11" pdb=" N   PRO A 117 "
      ideal   model   delta    sigma   weight residual
     116.90  131.46  -14.56 1.50e+00 4.44e-01 9.42e+01
  angle model="  11" pdb=" N   ARG A 129 "
        model="  11" pdb=" CA  ARG A 129 "
        model="  11" pdb=" CB  ARG A 129 "
      ideal   model   delta    sigma   weight residual
     110.50  125.93  -15.43 1.70e+00 3.46e-01 8.24e+01
  angle model="  11" pdb=" C   MET A 128 "
        model="  11" pdb=" CA  MET A 128 "
        model="  11" pdb=" CB  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.10  125.19  -15.09 1.90e+00 2.77e-01 6.31e+01
  angle model="  11" pdb=" CA  ILE A  51 "
        model="  11" pdb=" C   ILE A  51 "
        model="  11" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  128.73  -11.83 1.50e+00 4.44e-01 6.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.93: 938
       22.93 -    45.85: 69
       45.85 -    68.78: 18
       68.78 -    91.71: 7
       91.71 -   114.64: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  11" pdb=" CA  ARG A 127 "
           model="  11" pdb=" C   ARG A 127 "
           model="  11" pdb=" N   MET A 128 "
           model="  11" pdb=" CA  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -65.36 -114.64     0      5.00e+00 4.00e-02 5.26e+02
  dihedral model="  11" pdb=" C   ARG A 127 "
           model="  11" pdb=" N   ARG A 127 "
           model="  11" pdb=" CA  ARG A 127 "
           model="  11" pdb=" CB  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -155.35   32.75     0      2.50e+00 1.60e-01 1.72e+02
  dihedral model="  11" pdb=" N   ARG A 127 "
           model="  11" pdb=" C   ARG A 127 "
           model="  11" pdb=" CA  ARG A 127 "
           model="  11" pdb=" CB  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  154.57  -31.77     0      2.50e+00 1.60e-01 1.62e+02
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.278: 172
       0.278 -    0.555: 3
       0.555 -    0.832: 0
       0.832 -    1.109: 0
       1.109 -    1.387: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  ARG A 127 "
            model="  11" pdb=" N   ARG A 127 "
            model="  11" pdb=" C   ARG A 127 "
            model="  11" pdb=" CB  ARG A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.12    1.39 2.00e-01 2.50e+01 4.81e+01
  chirality model="  11" pdb=" CA  SER A  90 "
            model="  11" pdb=" N   SER A  90 "
            model="  11" pdb=" C   SER A  90 "
            model="  11" pdb=" CB  SER A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.83e+00
  chirality model="  11" pdb=" CA  ILE A  51 "
            model="  11" pdb=" N   ILE A  51 "
            model="  11" pdb=" C   ILE A  51 "
            model="  11" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.34 2.00e-01 2.50e+01 2.85e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  12 "   -0.152 2.00e-02 2.50e+03   7.01e-02 1.47e+02
        model="  11" pdb=" CG  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  12 "    0.032 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  12 "    0.028 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  12 "    0.025 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  12 "    0.028 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  12 "   -0.150 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  12 "    0.062 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  12 "    0.050 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  12 "    0.036 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  12 "    0.046 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  50 "   -0.099 2.00e-02 2.50e+03   6.94e-02 1.44e+02
        model="  11" pdb=" CG  TYR A  50 "   -0.033 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  50 "    0.036 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  50 "    0.031 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  50 "   -0.167 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  50 "    0.041 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  50 "    0.092 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  50 "    0.074 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  PHE A  15 "   -0.087 2.00e-02 2.50e+03   6.79e-02 1.38e+02
        model="  11" pdb=" CG  PHE A  15 "    0.039 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 PHE A  15 "    0.057 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 PHE A  15 "   -0.006 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 PHE A  15 "   -0.039 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 PHE A  15 "    0.024 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  PHE A  15 "   -0.002 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 PHE A  15 "    0.133 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 PHE A  15 "   -0.057 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 PHE A  15 "   -0.128 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 PHE A  15 "    0.061 2.00e-02 2.50e+03
        model="  11" pdb=" HZ  PHE A  15 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 192
        2.21 -     2.81: 4500
        2.81 -     3.41: 5894
        3.41 -     4.00: 7197
        4.00 -     4.60: 10839
  Nonbonded interactions: 28622
  Sorted by model distance:
  nonbonded model="  11" pdb=" HG2 ARG A 127 "
            model="  11" pdb=" H   ARG A 129 "
     model   vdw
     1.618 2.270
  nonbonded model="  11" pdb=" HA  ARG A 127 "
            model="  11" pdb=" H   ARG A 129 "
     model   vdw
     1.699 2.270
  nonbonded model="  11" pdb=" OD2 ASP A  44 "
            model="  11" pdb=" HG  SER A  46 "
     model   vdw
     1.707 1.850
  nonbonded model="  11" pdb=" HB3 LEU A  70 "
            model="  11" pdb="HD11 LEU A  99 "
     model   vdw
     1.729 2.440
  nonbonded model="  11" pdb=" HG2 ARG A 127 "
            model="  11" pdb=" HA  MET A 128 "
     model   vdw
     1.765 2.440
  ... (remaining 28617 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A LEU    3": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.68 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.415, 42.061, 48.455, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  PRO A  22 "
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ASP A  74 "
        model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CB  TYR A  89 "
        model="   2" pdb=" CB  LEU A  99 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.459  0.032 2.10e-02 2.27e+03 2.39e+00
  bond model="   9" pdb=" NE  ARG A 127 "
       model="   9" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 5.86e-02
  bond model="   9" pdb=" CZ  ARG A 129 "
       model="   9" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.57e-02
  bond model="   9" pdb=" CZ  ARG A 129 "
       model="   9" pdb=" NH1 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.01e-02
  bond model="   9" pdb=" CZ  ARG A  58 "
       model="   9" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 4.90e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.90 -   106.90: 70
      106.90 -   112.91: 2715
      112.91 -   118.91: 426
      118.91 -   124.91: 824
      124.91 -   130.91: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A  22 "
        model="   9" pdb=" CA  PRO A  22 "
        model="   9" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.86   -4.86 3.00e+00 1.11e-01 2.63e+00
  angle model="   9" pdb=" CB  PRO A 114 "
        model="   9" pdb=" CA  PRO A 114 "
        model="   9" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.85   -4.85 3.00e+00 1.11e-01 2.61e+00
  angle model="   9" pdb=" CB  PRO A 102 "
        model="   9" pdb=" CA  PRO A 102 "
        model="   9" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.84   -4.84 3.00e+00 1.11e-01 2.60e+00
  angle model="   9" pdb=" CB  PRO A  52 "
        model="   9" pdb=" CA  PRO A  52 "
        model="   9" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A   6 "
        model="   9" pdb=" CA  PRO A   6 "
        model="   9" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 877
       17.86 -    35.73: 79
       35.73 -    53.59: 48
       53.59 -    71.46: 24
       71.46 -    89.32: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CA  ASP A   7 "
           model="   9" pdb=" CB  ASP A   7 "
           model="   9" pdb=" CG  ASP A   7 "
           model="   9" pdb=" OD1 ASP A   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.81   58.81     1      2.00e+01 2.50e-03 1.16e+01
  dihedral model="   9" pdb=" CB  GLU A   8 "
           model="   9" pdb=" CG  GLU A   8 "
           model="   9" pdb=" CD  GLU A   8 "
           model="   9" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.32   89.32     1      3.00e+01 1.11e-03 1.05e+01
  dihedral model="   9" pdb=" CB  GLU A  16 "
           model="   9" pdb=" CG  GLU A  16 "
           model="   9" pdb=" CD  GLU A  16 "
           model="   9" pdb=" OE1 GLU A  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.69   85.69     1      3.00e+01 1.11e-03 9.86e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 90
       0.019 -    0.038: 62
       0.038 -    0.057: 5
       0.057 -    0.075: 0
       0.075 -    0.094: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A  37 "
            model="   9" pdb=" N   ILE A  37 "
            model="   9" pdb=" C   ILE A  37 "
            model="   9" pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.22e-01
  chirality model="   9" pdb=" CA  ILE A  51 "
            model="   9" pdb=" N   ILE A  51 "
            model="   9" pdb=" C   ILE A  51 "
            model="   9" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.19e-01
  chirality model="   9" pdb=" CA  ILE A  71 "
            model="   9" pdb=" N   ILE A  71 "
            model="   9" pdb=" C   ILE A  71 "
            model="   9" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.17e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  12 "    0.000 2.00e-02 2.50e+03   1.51e-03 6.83e-02
        model="   9" pdb=" CG  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  15 "   -0.000 2.00e-02 2.50e+03   1.31e-03 5.18e-02
        model="   9" pdb=" CG  PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  15 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  15 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  15 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  15 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  67 "   -0.000 2.00e-02 2.50e+03   1.29e-03 5.01e-02
        model="   9" pdb=" CG  PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  67 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  67 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  67 "    0.003 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 166
        2.16 -     2.77: 4313
        2.77 -     3.38: 5852
        3.38 -     3.99: 7038
        3.99 -     4.60: 10656
  Nonbonded interactions: 28025
  Sorted by model distance:
  nonbonded model="   9" pdb="HG12 VAL A  41 "
            model="   9" pdb="HG22 VAL A 112 "
     model   vdw
     1.547 2.440
  nonbonded model="   9" pdb="HD13 LEU A   3 "
            model="   9" pdb="HD22 LEU A  53 "
     model   vdw
     1.617 2.440
  nonbonded model="   9" pdb="HG23 ILE A  37 "
            model="   9" pdb="HD13 ILE A 108 "
     model   vdw
     1.666 2.440
  nonbonded model="   9" pdb="HD23 LEU A   9 "
            model="   9" pdb="HD22 LEU A  26 "
     model   vdw
     1.680 2.440
  nonbonded model="   9" pdb="HG22 VAL A  18 "
            model="   9" pdb=" HB3 ALA A  69 "
     model   vdw
     1.682 2.440
  ... (remaining 28020 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.74, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (58.558, 48.27, 48.709, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 91
        1.23 -     1.43: 387
        1.43 -     1.63: 653
        1.63 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" N   GLY A  80 "
       model="   2" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.571 -0.120 1.60e-02 3.91e+03 5.60e+01
  bond model="   2" pdb=" CA  LEU A  93 "
       model="   2" pdb=" CB  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.633 -0.103 2.00e-02 2.50e+03 2.64e+01
  bond model="   2" pdb=" CA  THR A  92 "
       model="   2" pdb=" C   THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.525  1.430  0.095 2.10e-02 2.27e+03 2.04e+01
  bond model="   2" pdb=" C   GLY A  94 "
       model="   2" pdb=" N   ASP A  95 "
    ideal  model  delta    sigma   weight residual
    1.329  1.267  0.062 1.40e-02 5.10e+03 1.98e+01
  bond model="   2" pdb=" N   LEU A  93 "
       model="   2" pdb=" CA  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.458  1.376  0.082 1.90e-02 2.77e+03 1.88e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       63.62 -    79.14: 1
       79.14 -    94.67: 10
       94.67 -   110.20: 2169
      110.20 -   125.73: 1818
      125.73 -   141.26: 81
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" N   TYR A  81 "
        model="   2" pdb=" CA  TYR A  81 "
        model="   2" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     110.00   63.62   46.38 3.00e+00 1.11e-01 2.39e+02
  angle model="   2" pdb=" C   LEU A  93 "
        model="   2" pdb=" CA  LEU A  93 "
        model="   2" pdb=" CB  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.10   84.83   25.27 1.90e+00 2.77e-01 1.77e+02
  angle model="   2" pdb=" CB  LEU A  93 "
        model="   2" pdb=" CA  LEU A  93 "
        model="   2" pdb=" HA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     109.00  141.26  -32.26 3.00e+00 1.11e-01 1.16e+02
  angle model="   2" pdb=" C   LYS A  79 "
        model="   2" pdb=" CA  LYS A  79 "
        model="   2" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.10   90.27   19.83 1.90e+00 2.77e-01 1.09e+02
  angle model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CG  LYS A  79 "
        model="   2" pdb=" CD  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     111.30  134.65  -23.35 2.30e+00 1.89e-01 1.03e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.55: 935
       21.55 -    43.10: 62
       43.10 -    64.65: 19
       64.65 -    86.20: 1
       86.20 -   107.75: 4
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   2" pdb=" C   TYR A  81 "
           model="   2" pdb=" N   TYR A  81 "
           model="   2" pdb=" CA  TYR A  81 "
           model="   2" pdb=" CB  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -176.48   53.88     0      2.50e+00 1.60e-01 4.64e+02
  dihedral model="   2" pdb=" CA  GLY A  80 "
           model="   2" pdb=" C   GLY A  80 "
           model="   2" pdb=" N   TYR A  81 "
           model="   2" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -72.25 -107.75     0      5.00e+00 4.00e-02 4.64e+02
  dihedral model="   2" pdb=" N   TYR A  81 "
           model="   2" pdb=" C   TYR A  81 "
           model="   2" pdb=" CA  TYR A  81 "
           model="   2" pdb=" CB  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  176.57  -53.77     0      2.50e+00 1.60e-01 4.63e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.082: 169
       1.082 -    2.163: 0
       2.163 -    3.245: 1
       3.245 -    4.326: 3
       4.326 -    5.407: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CA  LYS A  79 "
            model="   2" pdb=" N   LYS A  79 "
            model="   2" pdb=" C   LYS A  79 "
            model="   2" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.90    5.41 2.00e-01 2.50e+01 7.31e+02
  chirality model="   2" pdb=" CA  LEU A  99 "
            model="   2" pdb=" N   LEU A  99 "
            model="   2" pdb=" C   LEU A  99 "
            model="   2" pdb=" CB  LEU A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.30    4.81 2.00e-01 2.50e+01 5.79e+02
  chirality model="   2" pdb=" CA  PRO A  22 "
            model="   2" pdb=" N   PRO A  22 "
            model="   2" pdb=" C   PRO A  22 "
            model="   2" pdb=" CB  PRO A  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72   -1.82    4.54 2.00e-01 2.50e+01 5.14e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  PHE A  67 "    0.087 2.00e-02 2.50e+03   7.02e-02 1.48e+02
        model="   2" pdb=" CG  PHE A  67 "    0.036 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 PHE A  67 "    0.009 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 PHE A  67 "   -0.042 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 PHE A  67 "   -0.040 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 PHE A  67 "    0.011 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  PHE A  67 "    0.037 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 PHE A  67 "    0.025 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 PHE A  67 "   -0.131 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 PHE A  67 "   -0.125 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 PHE A  67 "    0.030 2.00e-02 2.50e+03
        model="   2" pdb=" HZ  PHE A  67 "    0.104 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A 111 "   -0.104 2.00e-02 2.50e+03   4.45e-02 5.95e+01
        model="   2" pdb=" CG  TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A 111 "   -0.086 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A 111 "    0.036 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A 111 "    0.037 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A 111 "    0.025 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A 111 "    0.023 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  12 "    0.083 2.00e-02 2.50e+03   4.05e-02 4.93e+01
        model="   2" pdb=" CG  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  12 "    0.088 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  12 "   -0.038 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  12 "   -0.045 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 53
        2.03 -     2.67: 3143
        2.67 -     3.32: 6831
        3.32 -     3.96: 8422
        3.96 -     4.60: 12743
  Nonbonded interactions: 31192
  Sorted by model distance:
  nonbonded model="   2" pdb=" H   TYR A  81 "
            model="   2" pdb=" HA  TYR A  81 "
     model   vdw
     1.388 1.816
  nonbonded model="   2" pdb=" HB2 TYR A  91 "
            model="   2" pdb=" H   THR A  92 "
     model   vdw
     1.686 2.270
  nonbonded model="   2" pdb=" H   GLY A  94 "
            model="   2" pdb=" H   ASP A  95 "
     model   vdw
     1.782 2.100
  nonbonded model="   2" pdb=" HB2 LEU A  93 "
            model="   2" pdb=" HA3 GLY A  94 "
     model   vdw
     1.804 2.440
  nonbonded model="   2" pdb=" O   ILE A 122 "
            model="   2" pdb=" HZ3 LYS A 125 "
     model   vdw
     1.816 1.850
  ... (remaining 31187 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.553, 52.906, 45.302, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  ILE A  78 "
        model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CB  TYR A  89 "
        model="   5" pdb=" CB  THR A  92 "
        model="   5" pdb=" CB  ARG A 127 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.25 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.393, 67.647, 32.314, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (64.136, 60.127, 45.004, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 57
        1.23 -     1.43: 415
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" N   GLY A  80 "
       model="   5" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.563 -0.112 1.60e-02 3.91e+03 4.90e+01
  bond model="   5" pdb=" CA  LYS A  79 "
       model="   5" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.614 -0.089 2.10e-02 2.27e+03 1.81e+01
  bond model="   5" pdb=" CA  ILE A  78 "
       model="   5" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.437  0.088 2.10e-02 2.27e+03 1.75e+01
  bond model="   5" pdb=" C   ASP A  88 "
       model="   5" pdb=" N   TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.329  1.386 -0.057 1.40e-02 5.10e+03 1.63e+01
  bond model="   5" pdb=" CA  GLY A  80 "
       model="   5" pdb=" C   GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.516  1.446  0.070 1.80e-02 3.09e+03 1.49e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       45.50 -    63.79: 1
       63.79 -    82.08: 1
       82.08 -   100.37: 21
      100.37 -   118.66: 3120
      118.66 -   136.95: 936
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" C   TYR A  89 "
        model="   5" pdb=" CA  TYR A  89 "
        model="   5" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   45.50   63.50 3.00e+00 1.11e-01 4.48e+02
  angle model="   5" pdb=" N   SER A  90 "
        model="   5" pdb=" CA  SER A  90 "
        model="   5" pdb=" CB  SER A  90 "
      ideal   model   delta    sigma   weight residual
     110.50  127.58  -17.08 1.70e+00 3.46e-01 1.01e+02
  angle model="   5" pdb=" CB  SER A  90 "
        model="   5" pdb=" CA  SER A  90 "
        model="   5" pdb=" HA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     109.00   81.00   28.00 3.00e+00 1.11e-01 8.71e+01
  angle model="   5" pdb=" CB  TYR A  89 "
        model="   5" pdb=" CA  TYR A  89 "
        model="   5" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00  136.50  -27.50 3.00e+00 1.11e-01 8.40e+01
  angle model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CG  LYS A  79 "
        model="   5" pdb=" CD  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     111.30  131.09  -19.79 2.30e+00 1.89e-01 7.40e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.57: 923
       23.57 -    47.13: 80
       47.13 -    70.70: 11
       70.70 -    94.26: 4
       94.26 -   117.83: 3
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   5" pdb=" CA  SER A  90 "
           model="   5" pdb=" C   SER A  90 "
           model="   5" pdb=" N   TYR A  91 "
           model="   5" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   62.17  117.83     0      5.00e+00 4.00e-02 5.55e+02
  dihedral model="   5" pdb=" CA  THR A  92 "
           model="   5" pdb=" C   THR A  92 "
           model="   5" pdb=" N   LEU A  93 "
           model="   5" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -74.36 -105.64     0      5.00e+00 4.00e-02 4.46e+02
  dihedral model="   5" pdb=" CA  ILE A  51 "
           model="   5" pdb=" C   ILE A  51 "
           model="   5" pdb=" N   PRO A  52 "
           model="   5" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   84.18   95.82     0      5.00e+00 4.00e-02 3.67e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    1.177: 168
       1.177 -    2.353: 1
       2.353 -    3.528: 1
       3.528 -    4.704: 2
       4.704 -    5.879: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CA  LYS A  79 "
            model="   5" pdb=" N   LYS A  79 "
            model="   5" pdb=" C   LYS A  79 "
            model="   5" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.37    5.88 2.00e-01 2.50e+01 8.64e+02
  chirality model="   5" pdb=" CB  ILE A  78 "
            model="   5" pdb=" CA  ILE A  78 "
            model="   5" pdb=" CG1 ILE A  78 "
            model="   5" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.93    5.57 2.00e-01 2.50e+01 7.76e+02
  chirality model="   5" pdb=" CA  ARG A 127 "
            model="   5" pdb=" N   ARG A 127 "
            model="   5" pdb=" C   ARG A 127 "
            model="   5" pdb=" CB  ARG A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.46    4.97 2.00e-01 2.50e+01 6.17e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  12 "    0.112 2.00e-02 2.50e+03   5.01e-02 7.52e+01
        model="   5" pdb=" CG  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  12 "   -0.026 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  12 "    0.103 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  12 "   -0.048 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  12 "   -0.039 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  81 "    0.088 2.00e-02 2.50e+03   4.84e-02 7.04e+01
        model="   5" pdb=" CG  TYR A  81 "   -0.010 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  81 "   -0.027 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  81 "   -0.030 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  81 "   -0.010 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  81 "    0.006 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  81 "    0.105 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  81 "    0.013 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  81 "   -0.050 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  81 "   -0.070 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  81 "   -0.010 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A 111 "   -0.074 2.00e-02 2.50e+03   4.04e-02 4.91e+01
        model="   5" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A 111 "   -0.089 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A 111 "    0.041 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A 111 "    0.026 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A 111 "    0.049 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 83
        2.09 -     2.72: 3578
        2.72 -     3.34: 6618
        3.34 -     3.97: 8164
        3.97 -     4.60: 11964
  Nonbonded interactions: 30407
  Sorted by model distance:
  nonbonded model="   5" pdb=" HA  ILE A  77 "
            model="   5" pdb=" HB2 LYS A  79 "
     model   vdw
     1.462 2.440
  nonbonded model="   5" pdb=" H   GLY A  80 "
            model="   5" pdb=" HA  TYR A  81 "
     model   vdw
     1.483 2.270
  nonbonded model="   5" pdb=" HA  ARG A 127 "
            model="   5" pdb=" H   ARG A 129 "
     model   vdw
     1.582 2.270
  nonbonded model="   5" pdb=" H   THR A  82 "
            model="   5" pdb=" H   THR A  83 "
     model   vdw
     1.658 2.100
  nonbonded model="   5" pdb=" HB  ILE A  78 "
            model="   5" pdb=" H   LYS A  79 "
     model   vdw
     1.688 2.270
  ... (remaining 30402 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (64.608, 61.202, 47.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  10" pdb=" CB  LYS A 125 "
  Number of C-beta restraints generated:  262

  Time building geometry restraints manager: 1.12 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 96
        1.23 -     1.43: 376
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH1 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.323  1.276  0.047 1.40e-02 5.10e+03 1.15e+01
  bond model="  10" pdb=" CZ  ARG A 129 "
       model="  10" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.47e+00
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.30e+00
  bond model="  10" pdb=" CZ  ARG A  58 "
       model="  10" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.44e+00
  bond model="  10" pdb=" CD2 HIS A 137 "
       model="  10" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.16e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       97.53 -   104.03: 28
      104.03 -   110.53: 2216
      110.53 -   117.03: 799
      117.03 -   123.53: 882
      123.53 -   130.03: 154
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  10" pdb=" C   ALA A 124 "
        model="  10" pdb=" N   LYS A 125 "
        model="  10" pdb=" CA  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     121.70  130.03   -8.33 1.80e+00 3.09e-01 2.14e+01
  angle model="  10" pdb=" OE1 GLN A  66 "
        model="  10" pdb=" CD  GLN A  66 "
        model="  10" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.13    4.47 1.00e+00 1.00e+00 2.00e+01
  angle model="  10" pdb=" CB  HIS A 135 "
        model="  10" pdb=" CG  HIS A 135 "
        model="  10" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.09    5.11 1.30e+00 5.92e-01 1.54e+01
  angle model="  10" pdb=" NE  ARG A  21 "
        model="  10" pdb=" CZ  ARG A  21 "
        model="  10" pdb=" NH2 ARG A  21 "
      ideal   model   delta    sigma   weight residual
     119.20  122.65   -3.45 9.00e-01 1.23e+00 1.47e+01
  angle model="  10" pdb=" C   LYS A 125 "
        model="  10" pdb=" CA  LYS A 125 "
        model="  10" pdb=" HA  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     109.00   97.53   11.47 3.00e+00 1.11e-01 1.46e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 949
       17.77 -    35.54: 50
       35.54 -    53.31: 19
       53.31 -    71.09: 8
       71.09 -    88.86: 5
  Dihedral angle restraints: 1031
    sinusoidal: 562
      harmonic: 469
  Sorted by residual:
  dihedral model="  10" pdb=" CA  LYS A 125 "
           model="  10" pdb=" C   LYS A 125 "
           model="  10" pdb=" N   VAL A 126 "
           model="  10" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -139.65  -40.35     0      5.00e+00 4.00e-02 6.51e+01
  dihedral model="  10" pdb=" CA  HIS A 134 "
           model="  10" pdb=" C   HIS A 134 "
           model="  10" pdb=" N   HIS A 135 "
           model="  10" pdb=" CA  HIS A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.71   22.29     0      5.00e+00 4.00e-02 1.99e+01
  dihedral model="  10" pdb=" CA  SER A  98 "
           model="  10" pdb=" C   SER A  98 "
           model="  10" pdb=" N   LEU A  99 "
           model="  10" pdb=" CA  LEU A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.70  -21.30     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 1028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.823: 175
       0.823 -    1.645: 0
       1.645 -    2.468: 0
       2.468 -    3.290: 0
       3.290 -    4.113: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CA  LYS A 125 "
            model="  10" pdb=" N   LYS A 125 "
            model="  10" pdb=" C   LYS A 125 "
            model="  10" pdb=" CB  LYS A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.60    4.11 2.00e-01 2.50e+01 4.23e+02
  chirality model="  10" pdb=" CA  HIS A 134 "
            model="  10" pdb=" N   HIS A 134 "
            model="  10" pdb=" C   HIS A 134 "
            model="  10" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality model="  10" pdb=" CA  GLU A 133 "
            model="  10" pdb=" N   GLU A 133 "
            model="  10" pdb=" C   GLU A 133 "
            model="  10" pdb=" CB  GLU A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.95e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  50 "   -0.225 2.00e-02 2.50e+03   1.03e-01 3.21e+02
        model="  10" pdb=" CG  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  50 "    0.039 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  50 "    0.051 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  50 "    0.044 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  50 "    0.032 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  50 "   -0.219 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  50 "    0.061 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  50 "    0.098 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  50 "    0.083 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  50 "    0.048 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  12 "   -0.121 2.00e-02 2.50e+03   5.58e-02 9.35e+01
        model="  10" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  12 "   -0.119 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  12 "    0.045 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  12 "    0.043 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  12 "    0.037 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  12 "    0.038 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  91 "    0.110 2.00e-02 2.50e+03   5.09e-02 7.79e+01
        model="  10" pdb=" CG  TYR A  91 "   -0.012 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  91 "   -0.038 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  91 "   -0.011 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  91 "   -0.024 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  91 "    0.016 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  91 "    0.077 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  91 "   -0.082 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  91 "    0.021 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  91 "   -0.059 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.38: 854
        2.38 -     2.94: 4944
        2.94 -     3.49: 5285
        3.49 -     4.05: 6780
        4.05 -     4.60: 10111
  Nonbonded interactions: 27974
  Sorted by model distance:
  nonbonded model="  10" pdb=" OD1 ASP A  36 "
            model="  10" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.830 1.850
  nonbonded model="  10" pdb=" OE1 GLU A  16 "
            model="  10" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.835 1.850
  nonbonded model="  10" pdb=" O   ILE A  30 "
            model="  10" pdb=" HG1 THR A  34 "
     model   vdw
     1.848 1.850
  nonbonded model="  10" pdb=" OD1 ASP A   7 "
            model="  10" pdb=" HZ1 LYS A  10 "
     model   vdw
     1.856 1.850
  nonbonded model="  10" pdb=" OD2 ASP A  44 "
            model="  10" pdb=" HG  SER A  46 "
     model   vdw
     1.857 1.850
  ... (remaining 27969 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.04, per 1000 atoms: 0.47
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (53.492, 61.295, 66.041, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CB  ILE A  78 "
        model="   3" pdb=" CB  LYS A  79 "
        model="   3" pdb=" CB  TYR A  89 "
        model="   3" pdb=" CB  GLU A 123 "
        model="   3" pdb=" CB  ARG A 129 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  15"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CB  ILE A  78 "
        model="   6" pdb=" CB  LYS A  79 "
        model="   6" pdb=" CB  SER A  90 "
        model="   6" pdb=" CB  THR A  92 "
        model="   6" pdb=" CB  ARG A 127 "
        model="   6" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  250

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.587, 48.739, 42.878, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 41
        1.23 -     1.42: 434
        1.42 -     1.62: 656
        1.62 -     1.81: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   3" pdb=" N   MET A 128 "
       model="   3" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.565 -0.107 1.90e-02 2.77e+03 3.15e+01
  bond model="   3" pdb=" C   ILE A  78 "
       model="   3" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.402 -0.073 1.40e-02 5.10e+03 2.70e+01
  bond model="   3" pdb=" N   LYS A  79 "
       model="   3" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.555 -0.097 1.90e-02 2.77e+03 2.60e+01
  bond model="   3" pdb=" CA  ILE A  78 "
       model="   3" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.624 -0.099 2.10e-02 2.27e+03 2.20e+01
  bond model="   3" pdb=" N   GLU A 123 "
       model="   3" pdb=" CA  GLU A 123 "
    ideal  model  delta    sigma   weight residual
    1.458  1.400  0.058 1.90e-02 2.77e+03 9.25e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       68.57 -    81.76: 1
       81.76 -    94.96: 3
       94.96 -   108.16: 632
      108.16 -   121.35: 2971
      121.35 -   134.55: 472
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   3" pdb=" C   ILE A  77 "
        model="   3" pdb=" CA  ILE A  77 "
        model="   3" pdb=" HA  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     109.00   68.57   40.43 3.00e+00 1.11e-01 1.82e+02
  angle model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CA  ILE A  51 "
        model="   3" pdb=" HA  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   83.23   25.77 3.00e+00 1.11e-01 7.38e+01
  angle model="   3" pdb=" CA  ALA A 124 "
        model="   3" pdb=" C   ALA A 124 "
        model="   3" pdb=" N   LYS A 125 "
      ideal   model   delta    sigma   weight residual
     116.20  101.44   14.76 2.00e+00 2.50e-01 5.44e+01
  angle model="   3" pdb=" C   ILE A  51 "
        model="   3" pdb=" CA  ILE A  51 "
        model="   3" pdb=" HA  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   87.35   21.65 3.00e+00 1.11e-01 5.21e+01
  angle model="   3" pdb=" C   ILE A  78 "
        model="   3" pdb=" N   LYS A  79 "
        model="   3" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  134.55  -12.85 1.80e+00 3.09e-01 5.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.31: 959
       25.31 -    50.62: 52
       50.62 -    75.92: 8
       75.92 -   101.23: 1
      101.23 -   126.54: 1
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   3" pdb=" CA  ILE A  77 "
           model="   3" pdb=" C   ILE A  77 "
           model="   3" pdb=" N   ILE A  78 "
           model="   3" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   53.46  126.54     0      5.00e+00 4.00e-02 6.40e+02
  dihedral model="   3" pdb=" C   ILE A  77 "
           model="   3" pdb=" N   ILE A  77 "
           model="   3" pdb=" CA  ILE A  77 "
           model="   3" pdb=" CB  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -162.17   40.17     0      2.50e+00 1.60e-01 2.58e+02
  dihedral model="   3" pdb=" N   ILE A  77 "
           model="   3" pdb=" C   ILE A  77 "
           model="   3" pdb=" CA  ILE A  77 "
           model="   3" pdb=" CB  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  160.50  -37.10     0      2.50e+00 1.60e-01 2.20e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.125: 167
       1.125 -    2.250: 1
       2.250 -    3.374: 1
       3.374 -    4.499: 1
       4.499 -    5.624: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   3" pdb=" CA  LYS A  79 "
            model="   3" pdb=" N   LYS A  79 "
            model="   3" pdb=" C   LYS A  79 "
            model="   3" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.11    5.62 2.00e-01 2.50e+01 7.91e+02
  chirality model="   3" pdb=" CB  ILE A  78 "
            model="   3" pdb=" CA  ILE A  78 "
            model="   3" pdb=" CG1 ILE A  78 "
            model="   3" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.64    5.29 2.00e-01 2.50e+01 6.98e+02
  chirality model="   3" pdb=" CB  ILE A 131 "
            model="   3" pdb=" CA  ILE A 131 "
            model="   3" pdb=" CG1 ILE A 131 "
            model="   3" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.28    4.93 2.00e-01 2.50e+01 6.07e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  89 "    0.135 2.00e-02 2.50e+03   5.07e-02 7.70e+01
        model="   3" pdb=" CG  TYR A  89 "   -0.031 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  89 "   -0.032 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  89 "   -0.035 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  89 "    0.020 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  89 "    0.054 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  89 "   -0.050 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  89 "   -0.059 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  89 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A 111 "    0.100 2.00e-02 2.50e+03   4.00e-02 4.81e+01
        model="   3" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A 111 "   -0.023 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A 111 "    0.069 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A 111 "   -0.033 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A 111 "   -0.037 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  50 "    0.082 2.00e-02 2.50e+03   3.22e-02 3.11e+01
        model="   3" pdb=" CG  TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  50 "    0.055 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  50 "   -0.029 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  50 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 221
        2.22 -     2.82: 4552
        2.82 -     3.41: 6198
        3.41 -     4.01: 7606
        4.01 -     4.60: 11519
  Nonbonded interactions: 30096
  Sorted by model distance:
  nonbonded model="   3" pdb=" HA  ALA A 124 "
            model="   3" pdb=" H   LYS A 125 "
     model   vdw
     1.629 2.270
  nonbonded model="   3" pdb="HG23 ILE A  77 "
            model="   3" pdb=" H   THR A  92 "
     model   vdw
     1.721 2.270
  nonbonded model="   3" pdb=" HA  ILE A  51 "
            model="   3" pdb=" HB  ILE A  51 "
     model   vdw
     1.722 1.952
  nonbonded model="   3" pdb=" OD2 ASP A  44 "
            model="   3" pdb=" HG  SER A  46 "
     model   vdw
     1.757 1.850
  nonbonded model="   3" pdb=" OD1 ASP A  95 "
            model="   3" pdb=" HG  SER A  97 "
     model   vdw
     1.763 1.850
  ... (remaining 30091 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   8" pdb=" CB  ILE A  78 "
        model="   8" pdb=" CB  TYR A  81 "
        model="   8" pdb=" CB  THR A  92 "
        model="   8" pdb=" CB  VAL A 126 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 44
        1.23 -     1.42: 428
        1.42 -     1.62: 659
        1.62 -     1.81: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   6" pdb=" CA  ASP A  88 "
       model="   6" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.672 -0.147 2.10e-02 2.27e+03 4.90e+01
  bond model="   6" pdb=" N   SER A 130 "
       model="   6" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.571 -0.113 1.90e-02 2.77e+03 3.55e+01
  bond model="   6" pdb=" C   ARG A 129 "
       model="   6" pdb=" N   SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.329  1.412 -0.083 1.40e-02 5.10e+03 3.51e+01
  bond model="   6" pdb=" CA  GLY A  87 "
       model="   6" pdb=" C   GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.516  1.602 -0.086 1.80e-02 3.09e+03 2.30e+01
  bond model="   6" pdb=" N   ASP A  88 "
       model="   6" pdb=" CA  ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.458  1.537 -0.079 1.90e-02 2.77e+03 1.72e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       76.26 -    90.65: 4
       90.65 -   105.04: 128
      105.04 -   119.44: 3080
      119.44 -   133.83: 860
      133.83 -   148.23: 7
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   6" pdb=" C   MET A 128 "
        model="   6" pdb=" CA  MET A 128 "
        model="   6" pdb=" CB  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.10  137.16  -27.06 1.90e+00 2.77e-01 2.03e+02
  angle model="   6" pdb=" OG1 THR A  92 "
        model="   6" pdb=" CB  THR A  92 "
        model="   6" pdb=" CG2 THR A  92 "
      ideal   model   delta    sigma   weight residual
     109.30  136.19  -26.89 2.00e+00 2.50e-01 1.81e+02
  angle model="   6" pdb=" N   MET A 128 "
        model="   6" pdb=" CA  MET A 128 "
        model="   6" pdb=" HA  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.00  148.23  -38.23 3.00e+00 1.11e-01 1.62e+02
  angle model="   6" pdb=" N   MET A 128 "
        model="   6" pdb=" CA  MET A 128 "
        model="   6" pdb=" C   MET A 128 "
      ideal   model   delta    sigma   weight residual
     111.00   76.26   34.74 2.80e+00 1.28e-01 1.54e+02
  angle model="   6" pdb=" C   ILE A  77 "
        model="   6" pdb=" N   ILE A  78 "
        model="   6" pdb=" CA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     121.70  139.63  -17.93 1.80e+00 3.09e-01 9.92e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.76: 953
       25.76 -    51.51: 49
       51.51 -    77.27: 12
       77.27 -   103.02: 2
      103.02 -   128.78: 3
  Dihedral angle restraints: 1019
    sinusoidal: 562
      harmonic: 457
  Sorted by residual:
  dihedral model="   6" pdb=" CA  SER A  90 "
           model="   6" pdb=" C   SER A  90 "
           model="   6" pdb=" N   TYR A  91 "
           model="   6" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -51.22 -128.78     0      5.00e+00 4.00e-02 6.63e+02
  dihedral model="   6" pdb=" CA  TYR A  89 "
           model="   6" pdb=" C   TYR A  89 "
           model="   6" pdb=" N   SER A  90 "
           model="   6" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -55.69 -124.31     0      5.00e+00 4.00e-02 6.18e+02
  dihedral model="   6" pdb=" CA  LYS A  79 "
           model="   6" pdb=" C   LYS A  79 "
           model="   6" pdb=" N   GLY A  80 "
           model="   6" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   67.97  112.03     0      5.00e+00 4.00e-02 5.02e+02
  ... (remaining 1016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.176: 168
       1.176 -    2.352: 0
       2.352 -    3.527: 0
       3.527 -    4.703: 4
       4.7
  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
03 -    5.878: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CB  ILE A  78 "
            model="   6" pdb=" CA  ILE A  78 "
            model="   6" pdb=" CG1 ILE A  78 "
            model="   6" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -3.23    5.88 2.00e-01 2.50e+01 8.64e+02
  chirality model="   6" pdb=" CA  THR A  92 "
            model="   6" pdb=" N   THR A  92 "
            model="   6" pdb=" C   THR A  92 "
            model="   6" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.63    5.15 2.00e-01 2.50e+01 6.63e+02
  chirality model="   6" pdb=" CA  LYS A  79 "
            model="   6" pdb=" N   LYS A  79 "
            model="   6" pdb=" C   LYS A  79 "
            model="   6" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.60    5.11 2.00e-01 2.50e+01 6.54e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  50 "   -0.222 2.00e-02 2.50e+03   8.64e-02 2.24e+02
        model="   6" pdb=" CG  TYR A  50 "    0.043 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  50 "    0.051 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  50 "    0.050 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  50 "   -0.139 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  50 "    0.080 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  50 "    0.076 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  50 "    0.022 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  12 "   -0.115 2.00e-02 2.50e+03   5.02e-02 7.55e+01
        model="   6" pdb=" CG  TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  12 "   -0.100 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  12 "    0.052 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  12 "    0.041 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CA  ARG A 129 "    0.034 2.00e-02 2.50e+03   6.64e-02 4.41e+01
        model="   6" pdb=" C   ARG A 129 "   -0.115 2.00e-02 2.50e+03
        model="   6" pdb=" O   ARG A 129 "    0.043 2.00e-02 2.50e+03
        model="   6" pdb=" N   SER A 130 "    0.038 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 184
        2.17 -     2.78: 4183
        2.78 -     3.38: 6505
        3.38 -     3.99: 7786
        3.99 -     4.60: 11746
  Nonbonded interactions: 30404
  Sorted by model distance:
  nonbonded model="   6" pdb=" HG2 LYS A  79 "
            model="   6" pdb=" H   GLY A  94 "
     model   vdw
     1.563 2.270
  nonbonded model="   6" pdb=" HB3 LYS A  79 "
            model="   6" pdb=" HA  LEU A  93 "
     model   vdw
     1.657 2.440
  nonbonded model="   6" pdb=" H   ILE A  77 "
            model="   6" pdb="HG13 ILE A  77 "
     model   vdw
     1.663 2.270
  nonbonded model="   6" pdb=" HG3 LYS A  85 "
            model="   6" pdb=" HA  ASP A  88 "
     model   vdw
     1.696 2.440
  nonbonded model="   6" pdb="HD13 LEU A  93 "
            model="   6" pdb=" HB2 SER A  97 "
     model   vdw
     1.713 2.440
  ... (remaining 30399 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  12" pdb=" CB  LEU A 119 "
        model="  12" pdb=" CB  GLU A 120 "
        model="  12" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  258

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.672, 43.15, 54.812, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 49
        1.23 -     1.43: 427
        1.43 -     1.62: 655
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   8" pdb=" N   GLY A  80 "
       model="   8" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.557 -0.106 1.60e-02 3.91e+03 4.42e+01
  bond model="   8" pdb=" C   VAL A 126 "
       model="   8" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.253  0.076 1.40e-02 5.10e+03 2.98e+01
  bond model="   8" pdb=" CA  LYS A  79 "
       model="   8" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.620 -0.095 2.10e-02 2.27e+03 2.05e+01
  bond model="   8" pdb=" CA  THR A  92 "
       model="   8" pdb=" CB  THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.540  1.637 -0.097 2.70e-02 1.37e+03 1.29e+01
  bond model="   8" pdb=" N   SER A 130 "
       model="   8" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.525 -0.067 1.90e-02 2.77e+03 1.25e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       74.52 -    87.65: 2
       87.65 -   100.79: 29
      100.79 -   113.93: 2802
      113.93 -   127.07: 1216
      127.07 -   140.21: 30
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   8" pdb=" N   TYR A  81 "
        model="   8" pdb=" CA  TYR A  81 "
        model="   8" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     110.00   74.52   35.48 3.00e+00 1.11e-01 1.40e+02
  angle model="   8" pdb=" C   VAL A 126 "
        model="   8" pdb=" N   ARG A 127 "
        model="   8" pdb=" CA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     121.70  101.34   20.36 1.80e+00 3.09e-01 1.28e+02
  angle model="   8" pdb=" N   TYR A  89 "
        model="   8" pdb=" CA  TYR A  89 "
        model="   8" pdb=" C   TYR A  89 "
      ideal   model   delta    sigma   weight residual
     111.00  140.21  -29.21 2.80e+00 1.28e-01 1.09e+02
  angle model="   8" pdb=" CB  TYR A  89 "
        model="   8" pdb=" CA  TYR A  89 "
        model="   8" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00  137.33  -28.33 3.00e+00 1.11e-01 8.92e+01
  angle model="   8" pdb=" N   TYR A  89 "
        model="   8" pdb=" CA  TYR A  89 "
        model="   8" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.00   81.84   28.16 3.00e+00 1.11e-01 8.81e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 915
       17.79 -    35.58: 75
       35.58 -    53.36: 23
       53.36 -    71.15: 7
       71.15 -    88.94: 5
  Dihedral angle restraints: 1025
    sinusoidal: 562
      harmonic: 463
  Sorted by residual:
  dihedral model="   8" pdb=" CA  GLY A  80 "
           model="   8" pdb=" C   GLY A  80 "
           model="   8" pdb=" N   TYR A  81 "
           model="   8" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   97.66   82.34     0      5.00e+00 4.00e-02 2.71e+02
  dihedral model="   8" pdb=" CA  VAL A 126 "
           model="   8" pdb=" C   VAL A 126 "
           model="   8" pdb=" N   ARG A 127 "
           model="   8" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  103.67   76.33     0      5.00e+00 4.00e-02 2.33e+02
  dihedral model="   8" pdb=" CA  ALA A 124 "
           model="   8" pdb=" C   ALA A 124 "
           model="   8" pdb=" N   LYS A 125 "
           model="   8" pdb=" CA  LYS A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  106.09   73.91     0      5.00e+00 4.00e-02 2.19e+02
  ... (remaining 1022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.005: 171
       1.005 -    2.009: 0
       2.009 -    3.013: 0
       3.013 -    4.018: 1
       4.018 -    5.022: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  VAL A 126 "
            model="   8" pdb=" N   VAL A 126 "
            model="   8" pdb=" C   VAL A 126 "
            model="   8" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44   -2.58    5.02 2.00e-01 2.50e+01 6.31e+02
  chirality model="   8" pdb=" CB  ILE A  78 "
            model="   8" pdb=" CA  ILE A  78 "
            model="   8" pdb=" CG1 ILE A  78 "
            model="   8" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.21    4.85 2.00e-01 2.50e+01 5.88e+02
  chirality model="   8" pdb=" CA  THR A  92 "
            model="   8" pdb=" N   THR A  92 "
            model="   8" pdb=" C   THR A  92 "
            model="   8" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.26    4.79 2.00e-01 2.50e+01 5.73e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  81 "   -0.172 2.00e-02 2.50e+03   1.25e-01 4.66e+02
        model="   8" pdb=" CG  TYR A  81 "   -0.011 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  81 "   -0.019 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  81 "    0.087 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  81 "    0.079 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  81 "   -0.020 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  81 "   -0.163 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  81 "   -0.091 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  81 "    0.230 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  81 "    0.208 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  81 "   -0.102 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  12 "   -0.119 2.00e-02 2.50e+03   5.14e-02 7.93e+01
        model="   8" pdb=" CG  TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  12 "    0.025 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  12 "   -0.103 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  12 "    0.041 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  12 "    0.038 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  12 "    0.027 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  12 "    0.030 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A 111 "    0.112 2.00e-02 2.50e+03   4.40e-02 5.80e+01
        model="   8" pdb=" CG  TYR A 111 "   -0.023 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A 111 "   -0.025 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A 111 "   -0.025 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A 111 "    0.073 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A 111 "   -0.037 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.13: 99
        2.13 -     2.75: 3907
  
  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
      2.75 -     3.37: 6376
        3.37 -     3.98: 7668
        3.98 -     4.60: 11738
  Nonbonded interactions: 29788
  Sorted by model distance:
  nonbonded model="   8" pdb="HG22 ILE A  77 "
            model="   8" pdb="HG23 ILE A  78 "
     model   vdw
     1.517 2.440
  nonbonded model="   8" pdb=" H   SER A  90 "
            model="   8" pdb=" HB2 TYR A  91 "
     model   vdw
     1.524 2.270
  nonbonded model="   8" pdb=" HA  LYS A  79 "
            model="   8" pdb=" HB3 TYR A  81 "
     model   vdw
     1.659 2.440
  nonbonded model="   8" pdb=" HA  ALA A 124 "
            model="   8" pdb=" H   VAL A 126 "
     model   vdw
     1.673 2.270
  nonbonded model="   8" pdb=" C   LYS A  79 "
            model="   8" pdb=" HA  TYR A  81 "
     model   vdw
     1.741 2.920
  ... (remaining 29783 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 77
        1.23 -     1.42: 395
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" CZ  ARG A 127 "
       model="  12" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.21e+01
  bond model="  12" pdb=" CD2 HIS A  43 "
       model="  12" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.374  1.406 -0.032 1.10e-02 8.26e+03 8.28e+00
  bond model="  12" pdb=" CB  THR A  83 "
       model="  12" pdb=" OG1 THR A  83 "
    ideal  model  delta    sigma   weight residual
    1.433  1.395  0.038 1.60e-02 3.91e+03 5.62e+00
  bond model="  12" pdb=" ND1 HIS A 139 "
       model="  12" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.36e+00
  bond model="  12" pdb=" CZ  ARG A  58 "
       model="  12" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.36e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       92.05 -    99.63: 7
       99.63 -   107.20: 445
      107.20 -   114.77: 2496
      114.77 -   122.34: 779
      122.34 -   129.91: 352
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" N   LEU A 119 "
        model="  12" pdb=" CA  LEU A 119 "
        model="  12" pdb=" C   LEU A 119 "
      ideal   model   delta    sigma   weight residual
     111.00  128.09  -17.09 2.80e+00 1.28e-01 3.72e+01
  angle model="  12" pdb=" N   LEU A 119 "
        model="  12" pdb=" CA  LEU A 119 "
        model="  12" pdb=" HA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     110.00   92.05   17.95 3.00e+00 1.11e-01 3.58e+01
  angle model="  12" pdb=" CA  LEU A 119 "
        model="  12" pdb=" C   LEU A 119 "
        model="  12" pdb=" N   GLU A 120 "
      ideal   model   delta    sigma   weight residual
     116.20  126.90  -10.70 2.00e+00 2.50e-01 2.86e+01
  angle model="  12" pdb=" CA  ASP A  88 "
        model="  12" pdb=" CB  ASP A  88 "
        model="  12" pdb=" CG  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     112.60  117.88   -5.28 1.00e+00 1.00e+00 2.78e+01
  angle model="  12" pdb=" CA  VAL A  41 "
        model="  12" pdb=" CB  VAL A  41 "
        model="  12" pdb=" CG1 VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.40  118.98   -8.58 1.70e+00 3.46e-01 2.55e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 910
       17.98 -    35.95: 67
       35.95 -    53.93: 37
       53.93 -    71.91: 5
       71.91 -    89.88: 8
  Dihedral angle restraints: 1027
    sinusoidal: 562
      harmonic: 465
  Sorted by residual:
  dihedral model="  12" pdb=" C   ARG A 129 "
           model="  12" pdb=" N   ARG A 129 "
           model="  12" pdb=" CA  ARG A 129 "
           model="  12" pdb=" CB  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -149.30   26.70     0      2.50e+00 1.60e-01 1.14e+02
  dihedral model="  12" pdb=" N   ARG A 129 "
           model="  12" pdb=" C   ARG A 129 "
           model="  12" pdb=" CA  ARG A 129 "
           model="  12" pdb=" CB  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  148.13  -25.33     0      2.50e+00 1.60e-01 1.03e+02
  dihedral model="  12" pdb=" CA  MET A 128 "
           model="  12" pdb=" C   MET A 128 "
           model="  12" pdb=" N   ARG A 129 "
           model="  12" pdb=" CA  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.44  -43.56     0      5.00e+00 4.00e-02 7.59e+01
  ... (remaining 1024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.916: 172
       0.916 -    1.830: 1
       1.830 -    2.745: 0
       2.745 -    3.660: 0
       3.660 -    4.575: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  MET A 128 "
            model="  12" pdb=" N   MET A 128 "
            model="  12" pdb=" C   MET A 128 "
            model="  12" pdb=" CB  MET A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.06    4.57 2.00e-01 2.50e+01 5.23e+02
  chirality model="  12" pdb=" CA  GLU A 120 "
            model="  12" pdb=" N   GLU A 120 "
            model="  12" pdb=" C   GLU A 120 "
            model="  12" pdb=" CB  GLU A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.97    4.49 2.00e-01 2.50e+01 5.03e+02
  chirality model="  12" pdb=" CA  LEU A 119 "
            model="  12" pdb=" N   LEU A 119 "
            model="  12" pdb=" C   LEU A 119 "
            model="  12" pdb=" CB  LEU A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.69    4.20 2.00e-01 2.50e+01 4.41e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A 111 "    0.160 2.00e-02 2.50e+03   6.34e-02 1.21e+02
        model="  12" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A 111 "   -0.036 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A 111 "   -0.036 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A 111 "    0.101 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A 111 "   -0.064 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A 111 "   -0.065 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  89 "   -0.096 2.00e-02 2.50e+03   5.52e-02 9.15e+01
        model="  12" pdb=" CG  TYR A  89 "   -0.026 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  89 "    0.040 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  89 "    0.021 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  89 "   -0.028 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  89 "   -0.044 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  89 "    0.123 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  89 "    0.009 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  89 "   -0.047 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  89 "    0.064 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  PHE A  67 "    0.127 2.00e-02 2.50e+03   5.52e-02 9.14e+01
        model="  12" pdb=" CG  PHE A  67 "   -0.014 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 PHE A  67 "   -0.031 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 PHE A  67 "   -0.027 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 PHE A  67 "   -0.010 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 PHE A  67 "   -0.014 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  PHE A  67 "    0.035 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 PHE A  67 "   -0.058 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 PHE A  67 "   -0.045 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 PHE A  67 "   -0.025 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 PHE A  67 "   -0.037 2.00e-02 2.50e+03
        model="  12" pdb=" HZ  PHE A  67 "    0.098 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 125
        2.12 -     2.74: 3876
        2.74 -     3.36: 6212
        3.36 -     3.98: 7662
        3.98 -     4.60: 11679
  Nonbonded interactions: 29554
  Sorted by model distance:
  nonbonded model="  12" pdb=" H   LYS A  85 "
            model="  12" pdb=" HD3 LYS A  85 "
     model   vdw
     1.504 2.270
  nonbonded model="  12" pdb="HG22 VAL A  41 "
            model="  12" pdb=" HA  GLU A 120 "
     model   vdw
     1.724 2.440
  nonbonded model="  12" pdb=" HB3 LYS A  85 "
            model="  12" pdb="HG22 ILE A 131 "
     model   vdw
     1.740 2.440
  nonbonded model="  12" pdb=" OD1 ASP A 103 "
            model="  12" pdb=" HZ3 LYS A 125 "
     model   vdw
     1.779 1.850
  nonbonded model="  12" pdb=" HZ2 LYS A  10 "
            model="  12" pdb=" OD1 ASP A  23 "
     model   vdw
     1.779 1.850
  ... (remaining 29549 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  PRO A  52 "
        model="   6" pdb=" CB  ILE A  78 "
        model="   6" pdb=" CB  LYS A  79 "
        model="   6" pdb=" CB  THR A  83 "
        model="   6" pdb=" CB  ASP A  88 "
        model="   6" pdb=" CB  TYR A  91 "
        model="   6" pdb=" CB  GLU A 123 "
        model="   6" pdb=" CB  LYS A 125 "
        model="   6" pdb=" CB  VAL A 126 "
        model="   6" pdb=" CB  MET A 128 "
        model="   6" pdb=" CB  ARG A 129 "
        model="   6" pdb=" CB  SER A 130 "
        model="   6" pdb=" CB  HIS A 138 "
  Number of C-beta restraints generated:  238

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 55
        1.23 -     1.43: 425
        1.43 -     1.62: 649
        1.62 -     1.82: 7
  Bond restraints: 2242
  Sorted by residual:
  bond model="   6" pdb=" C   TYR A  89 "
       model="   6" pdb=" N   SER A  90 "
    ideal  model  delta    sigma   weight residual
    1.329  1.212  0.117 1.40e-02 5.10e+03 6.96e+01
  bond model="   6" pdb=" CA  ILE A  77 "
       model="   6" pdb=" C   ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.525  1.386  0.139 2.10e-02 2.27e+03 4.40e+01
  bond model="   6" pdb=" CA  GLY A 121 "
       model="   6" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.631 -0.115 1.80e-02 3.09e+03 4.05e+01
  bond model="   6" pdb=" N   ILE A 122 "
       model="   6" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.570 -0.112 1.90e-02 2.77e+03 3.45e+01
  bond model="   6" pdb=" CA  ASP A  88 "
       model="   6" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.641 -0.116 2.10e-02 2.27e+03 3.06e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       76.56 -    90.23: 8
       90.23 -   103.91: 85
      103.91 -   117.58: 2967
      117.58 -   131.26: 1009
      131.26 -   144.94: 10
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   6" pdb=" N   TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" CB  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.50   88.75   21.75 1.70e+00 3.46e-01 1.64e+02
  angle model="   6" pdb=" CB  TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00  144.94  -35.94 3.00e+00 1.11e-01 1.43e+02
  angle model="   6" pdb=" C   ALA A 124 "
        model="   6" pdb=" CA  ALA A 124 "
        model="   6" pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     110.50  127.40  -16.90 1.50e+00 4.44e-01 1.27e+02
  angle model="   6" pdb=" C   TYR A  89 "
        model="   6" pdb=" CA  TYR A  89 "
        model="   6" pdb=" CB  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.10   88.79   21.31 1.90e+00 2.77e-01 1.26e+02
  angle model="   6" pdb=" N   ASP A  88 "
        model="   6" pdb=" CA  ASP A  88 "
        model="   6" pdb=" HA  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     110.00   76.56   33.44 3.00e+00 1.11e-01 1.24e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.33: 911
       21.33 -    42.67: 61
       42.67 -    64.00: 23
       64.00 -    85.34: 5
       85.34 -   106.67: 7
  Dihedral angle restraints: 1007
    sinusoidal: 562
      harmonic: 445
  Sorted by residual:
  dihedral model="   6" pdb=" CA  ALA A 124 "
           model="   6" pdb=" C   ALA A 124 "
           model="   6" pdb=" N   LYS A 125 "
           model="   6" pdb=" CA  LYS A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   73.33  106.67     0      5.00e+00 4.00e-02 4.55e+02
  dihedral model="   6" pdb=" CA  GLU A 123 "
           model="   6" pdb=" C   GLU A 123 "
           model="   6" pdb=" N   ALA A 124 "
           model="   6" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -73.61 -106.39     0      5.00e+00 4.00e-02 4.53e+02
  dihedral model="   6" pdb=" CA  SER A  90 "
           model="   6" pdb=" C   SER A  90 "
           model="   6" pdb=" N   TYR A  91 "
           model="   6" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -74.52 -105.48     0      5.00e+00 4.00e-02 4.45e+02
  ... (remaining 1004 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    1.166: 162
       1.166 -    2.330: 1
       2.330 -    3.494: 1
       3.494 -    4.658: 4
       4.658 -    5.822: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CA  LYS A  79 "
            model="   6" pdb=" N   LYS A  79 "
            model="   6" pdb=" C   LYS A  79 "
            model="   6" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.31    5.82 2.00e-01 2.50e+01 8.47e+02
  chirality model="   6" pdb=" CA  VAL A 126 "
            model="   6" pdb=" N   VAL A 126 "
            model="   6" pdb=" C   VAL A 126 "
            model="   6" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44   -3.03    5.48 2.00e-01 2.50e+01 7.50e+02
  chirality model="   6" pdb=" CA  ILE A  78 "
            model="   6" pdb=" N   ILE A  78 "
            model="   6" pdb=" C   ILE A  78 "
            model="   6" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -2.79    5.23 2.00e-01 2.50e+01 6.83e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  50 "    0.109 2.00e-02 2.50e+03   6.04e-02 1.09e+02
        model="   6" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  50 "   -0.031 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  50 "   -0.030 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  50 "    0.150 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  50 "   -0.052 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  50 "   -0.051 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CA  VAL A 126 "   -0.042 2.00e-02 2.50e+03   8.75e-02 7.65e+01
        model="   6" pdb=" C   VAL A 126 "    0.151 2.00e-02 2.50e+03
        model="   6" pdb=" O   VAL A 126 "   -0.059 2.00e-02 2.50e+03
        model="   6" pdb=" N   ARG A 127 "   -0.050 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  12 "   -0.100 2.00e-02 2.50e+03   4.53e-02 6.17e+01
        model="   6" pdb=" CG  TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  12 "    0.026 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  12 "    0.022 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  12 "   -0.093 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  12 "    0.048 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  12 "    0.044 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 156
        2.15 -     2.77: 4053
        2.77 -     3.38: 6607
        3.38 -     3.99: 7699
        3.99 -     4.60: 11601
  Nonbonded interactions: 30116
  Sorted by model distance:
  nonbonded model="   6" pdb=" HA  VAL A 126 "
            model="   6" pdb=" H   MET A 128 "
     model   vdw
     1.543 2.270
  nonbonded model="   6" pdb=" H   ASP A  88 "
            model="   6" pdb=" HA  ASP A  88 "
     model   vdw
     1.554 1.816
  nonbonded model="   6" pdb=" OD1 ASP A  95 "
            model="   6" pdb=" HG  SER A  97 "
     model   vdw
     1.721 1.850
  nonbonded model="   6" pdb=" OD2 ASP A  74 "
            model="   6" pdb=" HG  SER A  76 "
     model   vdw
     1.759 1.850
  nonbonded model="   6" pdb=" HA3 GLY A  42 "
            model="   6" pdb=" H   HIS A  43 "
     model   vdw
     1.766 2.270
  ... (remaining 30111 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.69
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ILE A  78 "
        model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CB  TYR A  89 "
        model="   2" pdb=" CB  THR A  92 "
        model="   2" pdb=" CB  ILE A 122 "
        model="   2" pdb=" CB  GLU A 123 "
        model="   2" pdb=" CB  LYS A 125 "
        model="   2" pdb=" CB  ARG A 127 "
  Number of C-beta restraints generated:  246

  Time building geometry restraints manager: 0.77 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.12, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (60.759, 41.516, 55.302, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 59
        1.23 -     1.43: 414
        1.43 -     1.62: 658
        1.62 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" N   ARG A 129 "
       model="   2" pdb=" CA  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.458  1.595 -0.137 1.90e-02 2.77e+03 5.23e+01
  bond model="   2" pdb=" CA  ILE A  78 "
       model="   2" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.653 -0.128 2.10e-02 2.27e+03 3.70e+01
  bond model="   2" pdb=" N   ILE A  77 "
       model="   2" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.549 -0.091 1.90e-02 2.77e+03 2.31e+01
  bond model="   2" pdb=" N   VAL A 126 "
       model="   2" pdb=" CA  VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.549 -0.091 1.90e-02 2.77e+03 2.31e+01
  bond model="   2" pdb=" C   ILE A  78 "
       model="   2" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.390 -0.061 1.40e-02 5.10e+03 1.87e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       74.12 -    87.59: 4
       87.59 -   101.05: 33
      101.05 -   114.51: 2826
      114.51 -   127.97: 1191
      127.97 -   141.43: 25
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" N   ARG A 127 "
        model="   2" pdb=" CA  ARG A 127 "
        model="   2" pdb=" HA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     110.00   74.12   35.88 3.00e+00 1.11e-01 1.43e+02
  angle model="   2" pdb=" C   ARG A 129 "
        model="   2" pdb=" N   SER A 130 "
        model="   2" pdb=" CA  SER A 130 "
      ideal   model   delta    sigma   weight residual
     121.70  141.43  -19.73 1.80e+00 3.09e-01 1.20e+02
  angle model="   2" pdb=" CB  ARG A 127 "
        model="   2" pdb=" CA  ARG A 127 "
        model="   2" pdb=" HA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     109.00  137.38  -28.38 3.00e+00 1.11e-01 8.95e+01
  angle model="   2" pdb=" N   ARG A 127 "
        model="   2" pdb=" CA  ARG A 127 "
        model="   2" pdb=" C   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     111.00  137.04  -26.04 2.80e+00 1.28e-01 8.65e+01
  angle model="   2" pdb=" C   ILE A  78 "
        model="   2" pdb=" N   LYS A  79 "
        model="   2" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  137.65  -15.95 1.80e+00 3.09e-01 7.85e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.48: 950
       26.48 -    52.97: 48
       52.97 -    79.45: 12
       79.45 -   105.94: 2
      105.94 -   132.42: 3
  Dihedral angle restraints: 1015
    sinusoidal: 562
      harmonic: 453
  Sorted by residual:
  dihedral model="   2" pdb=" CA  MET A 128 "
           model="   2" pdb=" C   MET A 128 "
           model="   2" pdb=" N   ARG A 129 "
           model="   2" pdb=" CA  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   47.58  132.42     0      5.00e+00 4.00e-02 7.01e+02
  dihedral model="   2" pdb=" CA  THR A  92 "
           model="   2" pdb=" C   THR A  92 "
           model="   2" pdb=" N   LEU A  93 "
           model="   2" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -68.72 -111.28     0      5.00e+00 4.00e-02 4.95e+02
  dihedral model="   2" pdb=" CA  LYS A 125 "
           model="   2" pdb=" C   LYS A 125 "
           model="   2" pdb=" N   VAL A 126 "
           model="   2" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   73.45  106.55     0      5.00e+00 4.00e-02 4.54e+02
  ... (remaining 1012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.122: 165
       1.122 -    2.244: 0
       2.244 -    3.366: 1
       3.366 -    4.487: 2
       4.487 -    5.609: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CA  THR A  92 "
            model="   2" pdb=" N   THR A  92 "
            model="   2" pdb=" C   THR A  92 "
            model="   2" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -3.08    5.61 2.00e-01 2.50e+01 7.86e+02
  chirality model="   2" pdb=" CA  LYS A  79 "
            model="   2" pdb=" N   LYS A  79 "
            model="   2" pdb=" C   LYS A  79 "
            model="   2" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.04    5.55 2.00e-01 2.50e+01 7.70e+02
  chirality model="   2" pdb=" CA  GLU A 123 "
            model="   2" pdb=" N   GLU A 123 "
            model="   2" pdb=" C   GLU A 123 "
            model="   2" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.68    5.19 2.00e-01 2.50e+01 6.73e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  91 "    0.137 2.00e-02 2.50e+03   6.73e-02 1.36e+02
        model="   2" pdb=" CG  TYR A  91 "    0.038 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  91 "   -0.033 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  91 "   -0.020 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  91 "   -0.013 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  91 "   -0.025 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  91 "    0.026 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  91 "    0.123 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  91 "   -0.093 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  91 "   -0.056 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  91 "   -0.025 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  91 "   -0.061 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  HIS A  43 "   -0.129 2.00e-02 2.50e+03   7.80e-02 1.22e+02
        model="   2" pdb=" CG  HIS A  43 "    0.088 2.00e-02 2.50e+03
        model="   2" pdb=" ND1 HIS A  43 "    0.127 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 HIS A  43 "    0.022 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 HIS A  43 "   -0.010 2.00e-02 2.50e+03
        model="   2" pdb=" NE2 HIS A  43 "   -0.038 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 HIS A  43 "    0.018 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 HIS A  43 "   -0.077 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  89 "    0.077 2.00e-02 2.50e+03   5.38e-02 8.67e+01
        model="   2" pdb=" CG  TYR A  89 "    0.028 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  89 "   -0.029 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  89 "   -0.021 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  89 "    0.020 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  89 "    0.126 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  89 "   -0.038 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  89 "   -0.076 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  89 "   -0.052 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.09: 96
        2.09 -     2.72: 3600
        2.72 -     3.35: 6684
        3.35 -     3.97: 8116
        3.97 -     4.60: 12185
  Nonbonded interactions: 30681
  Sorted by model distance:
  nonbonded model="   2" pdb=" HA  ILE A  77 "
            model="   2" pdb=" H   LYS A  79 "
     model   vdw
     1.466 2.270
  nonbonded model="   2" pdb="HD12 LEU A  93 "
            model="   2" pdb=" H   GLY A  94 "
     model   vdw
     1.646 2.270
  nonbonded model="   2" pdb=" H   MET A 128 "
            model="   2" pdb=" HG3 MET A 128 "
     model   vdw
     1.746 2.270
  nonbonded model="   2" pdb=" O   TYR A  89 "
            model="   2" pdb=" HG  SER A  90 "
     model   vdw
     1.758 1.850
  nonbonded model="   2" pdb=" O   LEU A  61 "
            model="   2" pdb=" HG  SER A  65 "
     model   vdw
     1.776 1.850
  ... (remaining 30676 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (55.239, 43.618, 57.566, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.38, 41.696, 54.728, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  TYR A  89 "
        model="   7" pdb=" CB  THR A  92 "
        model="   7" pdb=" CB  SER A  97 "
        model="   7" pdb=" CB  SER A  98 "
        model="   7" pdb=" CB  GLU A 123 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  ILE A  78 "
        model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CB  TYR A  89 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  LYS A  79 "
        model="   7" pdb=" CB  TYR A  81 "
        model="   7" pdb=" CB  TYR A  89 "
        model="   7" pdb=" CB  PRO A 117 "
        model="   7" pdb=" CB  LEU A 119 "
        model="   7" pdb=" CB  ILE A 122 "
        model="   7" pdb=" CB  GLU A 123 "
        model="   7" pdb=" CB  LYS A 125 "
        model="   7" pdb=" CB  VAL A 126 "
        model="   7" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  242

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 72
        1.23 -     1.43: 405
        1.43 -     1.62: 653
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" CA  GLY A 121 "
       model="   7" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.640 -0.124 1.80e-02 3.09e+03 4.74e+01
  bond model="   7" pdb=" C   GLU A 123 "
       model="   7" pdb=" N   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.329  1.242  0.087 1.40e-02 5.10e+03 3.87e+01
  bond model="   7" pdb=" CA  ALA A 124 "
       model="   7" pdb=" C   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.525  1.633 -0.108 2.10e-02 2.27e+03 2.66e+01
  bond model="   7" pdb=" N   ILE A 122 "
       model="   7" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.546 -0.088 1.90e-02 2.77e+03 2.14e+01
  bond model="   7" pdb=" N   VAL A 126 "
       model="   7" pdb=" CA  VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.535 -0.077 1.90e-02 2.77e+03 1.65e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       78.03 -    89.72: 3
       89.72 -   101.41: 27
      101.41 -   113.11: 2656
      113.11 -   124.80: 1286
      124.80 -   136.49: 107
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" CA  TYR A  81 "
        model="   7" pdb=" CB  TYR A  81 "
        model="   7" pdb=" CG  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     113.90  135.22  -21.32 1.80e+00 3.09e-01 1.40e+02
  angle model="   7" pdb=" C   THR A  82 "
        model="   7" pdb=" CA  THR A  82 "
        model="   7" pdb=" HA  THR A  82 "
      ideal   model   delta    sigma   weight residual
     109.00   78.03   30.97 3.00e+00 1.11e-01 1.07e+02
  angle model="   7" pdb=" C   ALA A 124 "
        model="   7" pdb=" CA  ALA A 124 "
        model="   7" pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     110.50  123.85  -13.35 1.50e+00 4.44e-01 7.92e+01
  angle model="   7" pdb=" N   TYR A  81 "
        model="   7" pdb=" CA  TYR A  81 "
        model="   7" pdb=" CB  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     110.50  124.89  -14.39 1.70e+00 3.46e-01 7.17e+01
  angle model="   7" pdb=" C   TYR A  91 "
        model="   7" pdb=" N   THR A  92 "
        model="   7" pdb=" CA  THR A  92 "
      ideal   model   delta    sigma   weight residual
     121.70  136.49  -14.79 1.80e+00 3.09e-01 6.76e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.81: 946
       24.81 -    49.63: 50
       49.63 -    74.44: 22
       74.44 -    99.26: 1
       99.26 -   124.07: 2
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   7" pdb=" CA  TYR A  91 "
           model="   7" pdb=" C   TYR A  91 "
           model="   7" pdb=" N   THR A  92 "
           model="   7" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   55.93  124.07     0      5.00e+00 4.00e-02 6.16e+02
  dihedral model="   7" pdb=" CA  GLU A 123 "
           model="   7" pdb=" C   GLU A 123 "
           model="   7" pdb=" N   ALA A 124 "
           model="   7" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   78.26  101.74     0      5.00e+00 4.00e-02 4.14e+02
  dihedral model="   7" pdb=" CA  TYR A  89 "
           model="   7" pdb=" C   TYR A  89 "
           model="   7" pdb=" N   SER A  90 "
           model="   7" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -86.42  -93.58     0      5.00e+00 4.00e-02 3.50e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.080: 166
       1.080 -    2.160: 1
       2.160 -    3.240: 0
       3.240 -    4.320: 0
       4.320 -    5.400: 9
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CA  THR A  92 "
            model="   7" pdb=" N   THR A  92 "
            model="   7" pdb=" C   THR A  92 "
            model="   7" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.87    5.40 2.00e-01 2.50e+01 7.29e+02
  chirality model="   7" pdb=" CB  THR A  92 "
            model="   7" pdb=" CA  THR A  92 "
            model="   7" pdb=" OG1 THR A  92 "
            model="   7" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.79    5.34 2.00e-01 2.50e+01 7.13e+02
  chirality model="   7" pdb=" CA  GLU A 123 "
            model="   7" pdb=" N   GLU A 123 "
            model="   7" pdb=" C   GLU A 123 "
            model="   7" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.82    5.33 2.00e-01 2.50e+01 7.11e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  81 "    0.379 2.00e-02 2.50e+03   1.46e-01 6.40e+02
        model="   7" pdb=" CG  TYR A  81 "   -0.061 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  81 "   -0.090 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  81 "   -0.083 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  81 "   -0.017 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  81 "   -0.035 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  81 "    0.049 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  81 "    0.213 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  81 "   -0.156 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  81 "   -0.129 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  81 "   -0.058 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  12 "    0.088 2.00e-02 2.50e+03   4.09e-02 5.01e+01
        model="   7" pdb=" CG  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  12 "    0.087 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  12 "   -0.039 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  12 "   -0.039 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CA  GLU A 123 "   -0.034 2.00e-02 2.50e+03   6.90e-02 4.76e+01
        model="   7" pdb=" C   GLU A 123 "    0.119 2.00e-02 2.50e+03
        model="   7" pdb=" O   GLU A 123 "   -0.046 2.00e-02 2.50e+03
        model="   7" pdb=" N   ALA A 124 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 107
        2.11 -     2.74: 3793
        2.74 -     3.36: 6754
        3.36 -     3.98: 8339
        3.98 -     4.60: 12615
  Nonbonded interactions: 31608
  Sorted by model distance:
  nonbonded model="   7" pdb=" HA  ALA A 124 "
            model="   7" pdb=" H   VAL A 126 "
     model   vdw
     1.493 2.270
  nonbonded model="   7" pdb=" H   LYS A  79 "
            model="   7" pdb=" HB2 TYR A  81 "
     model   vdw
     1.706 2.270
  nonbonded model="   7" pdb=" OD2 ASP A  44 "
            model="   7" pdb=" HG  SER A  46 "
     model   vdw
     1.720 1.850
  nonbonded model="   7" pdb=" HZ  PHE A  67 "
            model="   7" pdb=" HH  TYR A  81 "
     model   vdw
     1.773 2.100
  nonbonded model="   7" pdb=" H   LEU A  93 "
            model="   7" pdb=" HB3 SER A  98 "
     model   vdw
     1.775 2.270
  ... (remaining 31603 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 73
        1.23 -     1.43: 400
        1.43 -     1.62: 659
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" CA  LYS A  79 "
       model="   5" pdb=" CB  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.530  1.602 -0.072 2.00e-02 2.50e+03 1.28e+01
  bond model="   5" pdb=" N   GLY A  80 "
       model="   5" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.503 -0.052 1.60e-02 3.91e+03 1.04e+01
  bond model="   5" pdb=" CA  THR A  92 "
       model="   5" pdb=" C   THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.525  1.464  0.061 2.10e-02 2.27e+03 8.41e+00
  bond model="   5" pdb=" CD2 HIS A 139 "
       model="   5" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.63e+00
  bond model="   5" pdb=" CZ  ARG A  21 "
       model="   5" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.53e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       63.03 -    77.50: 1
       77.50 -    91.97: 1
       91.97 -   106.44: 198
      106.44 -   120.91: 3368
      120.91 -   135.37: 511
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" C   ILE A  78 "
        model="   5" pdb=" CA  ILE A  78 "
        model="   5" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   63.03   45.97 3.00e+00 1.11e-01 2.35e+02
  angle model="   5" pdb=" C   TYR A  89 "
        model="   5" pdb=" N   SER A  90 "
        model="   5" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  106.22   15.48 1.80e+00 3.09e-01 7.40e+01
  angle model="   5" pdb=" C   LYS A  79 "
        model="   5" pdb=" CA  LYS A  79 "
        model="   5" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.10   95.43   14.67 1.90e+00 2.77e-01 5.96e+01
  angle model="   5" pdb=" N   LYS A  79 "
        model="   5" pdb=" CA  LYS A  79 "
        model="   5" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.50   97.46   13.04 1.70e+00 3.46e-01 5.88e+01
  angle model="   5" pdb=" C   ILE A  78 "
        model="   5" pdb=" CA  ILE A  78 "
        model="   5" pdb=" CB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     111.60  126.87  -15.27 2.00e+00 2.50e-01 5.83e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.22: 962
       22.22 -    44.44: 45
       44.44 -    66.67: 10
       66.67 -    88.89: 4
       88.89 -   111.11: 4
  Dihedral angle restraints: 1025
    sinusoidal: 562
      harmonic: 463
  Sorted by residual:
  dihedral model="   5" pdb=" CA  LYS A  79 "
           model="   5" pdb=" C   LYS A  79 "
           model="   5" pdb=" N   GLY A  80 "
           model="   5" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -68.89 -111.11     0      5.00e+00 4.00e-02 4.94e+02
  dihedral model="   5" pdb=" CA  ILE A  77 "
           model="   5" pdb=" C   ILE A  77 "
           model="   5" pdb=" N   ILE A  78 "
           model="   5" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -85.12  -94.88     0      5.00e+00 4.00e-02 3.60e+02
  dihedral model="   5" pdb=" CA  SER A  90 "
           model="   5" pdb=" C   SER A  90 "
           model="   5" pdb=" N   TYR A  91 "
           model="   5" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  -87.65  -92.35     0      5.00e+00 4.00e-02 3.41e+02
  ... (remaining 1022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.189: 171
       1.189 -    2.377: 0
       2.377 -    3.566: 2
       3.566 -    4.754: 1
       4.754 -    5.942: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CA  LYS A  79 "
            model="   5" pdb=" N   LYS A  79 "
            model="   5" pdb=" C   LYS A  79 "
            model="   5" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.43    5.94 2.00e-01 2.50e+01 8.83e+02
  chirality model="   5" pdb=" CA  TYR A  89 "
            model="   5" pdb=" N   TYR A  89 "
            model="   5" pdb=" C   TYR A  89 "
            model="   5" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.33    4.84 2.00e-01 2.50e+01 5.87e+02
  chirality model="   5" pdb=" CB  ILE A  78 "
            model="   5" pdb=" CA  ILE A  78 "
            model="   5" pdb=" CG1 ILE A  78 "
            model="   5" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -1.50    4.14 2.00e-01 2.50e+01 4.29e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  91 "    0.501 2.00e-02 2.50e+03   2.29e-01 1.57e+03
        model="   5" pdb=" CG  TYR A  91 "    0.055 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  91 "   -0.093 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  91 "   -0.106 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  91 "   -0.076 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  91 "   -0.066 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  91 "    0.074 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  91 "    0.446 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  91 "   -0.201 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  91 "   -0.237 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  91 "   -0.165 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  91 "   -0.133 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  PHE A  67 "   -0.123 2.00e-02 2.50e+03   5.16e-02 7.99e+01
        model="   5" pdb=" CG  PHE A  67 "    0.036 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 PHE A  67 "    0.043 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 PHE A  67 "    0.020 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 PHE A  67 "   -0.007 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 PHE A  67 "    0.015 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  PHE A  67 "   -0.024 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 PHE A  67 "    0.080 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 PHE A  67 "    0.013 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 PHE A  67 "   -0.030 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 PHE A  67 "    0.037 2.00e-02 2.50e+03
        model="   5" pdb=" HZ  PHE A  67 "   -0.059 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  50 "   -0.102 2.00e-02 2.50e+03   4.32e-02 5.60e+01
        model="   5" pdb=" CG  TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  50 "   -0.080 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  50 "    0.045 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  50 "    0.031 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 91
        2.12 -     2.74: 3795
        2.74 -     3.36: 6492
        3.36 -     3.98: 8016
        3.98 -     4.60: 12043
  Nonbonded interactions: 30437
  Sorted by model distance:
  nonbonded model="   5" pdb=" HA  ILE A  77 "
            model="   5" pdb="HG22 ILE A  78 "
     model   vdw
     1.499 2.440
  nonbonded model="   5" pdb=" HA  LYS A  79 "
            model="   5" pdb=" H   THR A  82 "
     model   vdw
     1.580 2.270
  nonbonded model="   5" pdb=" HA  ILE A  78 "
            model="   5" pdb=" N   LYS A  79 "
     model   vdw
     1.729 2.216
  nonbonded model="   5" pdb=" HB  ILE A  78 "
            model="   5" pdb=" HB2 LYS A  79 "
     model   vdw
     1.757 2.440
  nonbonded model="   5" pdb=" HB3 LYS A  79 "
            model="   5" pdb=" HA3 GLY A  80 "
     model   vdw
     1.783 2.440
  ... (remaining 30432 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.06, per 1000 atoms: 0.48
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (48.795, 63.596, 51.601, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 57
        1.23 -     1.43: 420
        1.43 -     1.62: 653
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" N   GLY A  80 "
       model="   7" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.550 -0.099 1.60e-02 3.91e+03 3.82e+01
  bond model="   7" pdb=" N   SER A 130 "
       model="   7" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.571 -0.113 1.90e-02 2.77e+03 3.56e+01
  bond model="   7" pdb=" CA  ASP A  88 "
       model="   7" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.649 -0.124 2.10e-02 2.27e+03 3.50e+01
  bond model="   7" pdb=" N   LYS A 125 "
       model="   7" pdb=" CA  LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.566 -0.108 1.90e-02 2.77e+03 3.23e+01
  bond model="   7" pdb=" N   LEU A  93 "
       model="   7" pdb=" CA  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.458  1.358  0.100 1.90e-02 2.77e+03 2.79e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       82.25 -    93.49: 5
       93.49 -   104.72: 96
      104.72 -   115.96: 2884
      115.96 -   127.20: 1054
      127.20 -   138.44: 40
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" N   VAL A 126 "
        model="   7" pdb=" CA  VAL A 126 "
        model="   7" pdb=" CB  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     111.50   90.37   21.13 1.70e+00 3.46e-01 1.55e+02
  angle model="   7" pdb=" C   MET A 128 "
        model="   7" pdb=" CA  MET A 128 "
        model="   7" pdb=" CB  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.10  131.98  -21.88 1.90e+00 2.77e-01 1.33e+02
  angle model="   7" pdb=" CA  LYS A 125 "
        model="   7" pdb=" C   LYS A 125 "
        model="   7" pdb=" N   VAL A 126 "
      ideal   model   delta    sigma   weight residual
     116.20   94.84   21.36 2.00e+00 2.50e-01 1.14e+02
  angle model="   7" pdb=" O   VAL A 126 "
        model="   7" pdb=" C   VAL A 126 "
        model="   7" pdb=" N   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     123.00  106.05   16.95 1.60e+00 3.91e-01 1.12e+02
  angle model="   7" pdb=" C   TYR A  89 "
        model="   7" pdb=" N   SER A  90 "
        model="   7" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  103.07   18.63 1.80e+00 3.09e-01 1.07e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.76: 924
       24.76 -    49.51: 60
       49.51 -    74.27: 14
       74.27 -    99.03: 9
       99.03 -   123.78: 4
  Dihedral angle restraints: 1011
    sinusoidal: 562
      harmonic: 449
  Sorted by residual:
  dihedral model="   7" pdb=" CA  ARG A 127 "
           model="   7" pdb=" C   ARG A 127 "
           model="   7" pdb=" N   MET A 128 "
           model="   7" pdb=" CA  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   56.22  123.78     0      5.00e+00 4.00e-02 6.13e+02
  dihedral model="   7" pdb=" CA  ASP A 116 "
           model="   7" pdb=" C   ASP A 116 "
           model="   7" pdb=" N   PRO A 117 "
           model="   7" pdb=" CA  PRO A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   66.21  113.79     0      5.00e+00 4.00e-02 5.18e+02
  dihedral model="   7" pdb=" CA  GLU A 123 "
           model="   7" pdb=" C   GLU A 123 "
           model="   7" pdb=" N   ALA A 124 "
           model="   7" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   68.09  111.91     0      5.00e+00 4.00e-02 5.01e+02
  ... (remaining 1008 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.209: 162
       1.209 -    2.417: 0
       2.417 -    3.626: 2
       3.626 -    4.835: 4
       4.835 -    6.043: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CA  LYS A  79 "
            model="   7" pdb=" N   LYS A  79 "
            model="   7" pdb=" C   LYS A  79 "
            model="   7" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.53    6.04 2.00e-01 2.50e+01 9.13e+02
  chirality model="   7" pdb=" CB  THR A  92 "
            model="   7" pdb=" CA  THR A  92 "
            model="   7" pdb=" OG1 THR A  92 "
            model="   7" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -3.08    5.63 2.00e-01 2.50e+01 7.92e+02
  chirality model="   7" pdb=" CA  VAL A 126 "
            model="   7" pdb=" N   VAL A 126 "
            model="   7" pdb=" C   VAL A 126 "
            model="   7" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44   -3.14    5.58 2.00e-01 2.50e+01 7.77e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  91 "    0.034 2.00e-02 2.50e+03   5.74e-02 9.90e+01
        model="   7" pdb=" CG  TYR A  91 "   -0.091 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  91 "   -0.039 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  91 "    0.026 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  91 "   -0.023 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  91 "   -0.036 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  91 "   -0.009 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  91 "   -0.047 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  91 "    0.100 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  91 "    0.111 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  91 "   -0.036 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  12 "   -0.119 2.00e-02 2.50e+03   5.25e-02 8.26e+01
        model="   7" pdb=" CG  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  12 "    0.025 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  12 "    0.018 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  12 "   -0.108 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  12 "    0.040 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  12 "    0.043 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  12 "    0.033 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  12 "    0.029 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  HIS A  43 "    0.104 2.00e-02 2.50e+03   6.35e-02 8.07e+01
        model="   7" pdb=" CG  HIS A  43 "   -0.077 2.00e-02 2.50e+03
        model="   7" pdb=" ND1 HIS A  43 "   -0.100 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 HIS A  43 "   -0.018 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 HIS A  43 "    0.009 2.00e-02 2.50e+03
        model="   7" pdb=" NE2 HIS A  43 "    0.017 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 HIS A  43 "   -0.004 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 HIS A  43 "    0.070 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 235
        2.20 -     2.80: 4443
        2.80 -     3.40: 6524
        3.40 -     4.00: 7886
        4.00 -     4.60: 11748
  Nonbonded interactions: 30836
  Sorted by model distance:
  nonbonded model="   7" pdb=" HA  SER A  76 "
            model="   7" pdb="HG23 ILE A  78 "
     model   vdw
     1.603 2.440
  nonbonded model="   7" pdb=" O   LYS A  79 "
            model="   7" pdb=" HA  TYR A  81 "
     model   vdw
     1.629 2.620
  nonbonded model="   7" pdb="HD11 LEU A  93 "
            model="   7" pdb=" HA  SER A  98 "
     model   vdw
     1.633 2.440
  nonbonded model="   7" pdb=" H   THR A  92 "
            model="   7" pdb="HG23 THR A  92 "
     model   vdw
     1.660 2.270
  nonbonded model="   7" pdb="HG23 ILE A  77 "
            model="   7" pdb="HG21 THR A  83 "
     model   vdw
     1.674 2.440
  ... (remaining 30831 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  ILE A  77 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CB  LYS A  79 "
        model="   4" pdb=" CB  THR A  92 "
        model="   4" pdb=" CB  SER A  97 "
        model="   4" pdb=" CB  ILE A 122 "
        model="   4" pdb=" CB  GLU A 123 "
        model="   4" pdb=" CB  ALA A 124 "
        model="   4" pdb=" CB  ILE A 131 "
  Number of C-beta restraints generated:  244

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CB  LYS A  79 "
        model="   6" pdb=" CB  TYR A  91 "
        model="   6" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1105
        1.04 -     1.23: 106
        1.23 -     1.43: 370
        1.43 -     1.63: 644
        1.63 -     1.82: 16
  Bond restraints: 2241
  Sorted by residual:
  bond model="   4" pdb=" N   MET A 128 "
       model="   4" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.824 -0.366 1.90e-02 2.77e+03 3.70e+02
  bond model="   4" pdb=" N   SER A 130 "
       model="   4" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.691 -0.233 1.90e-02 2.77e+03 1.50e+02
  bond model="   4" pdb=" CA  ILE A  78 "
       model="   4" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.749 -0.224 2.10e-02 2.27e+03 1.14e+02
  bond model="   4" pdb=" N   LEU A 132 "
       model="   4" pdb=" CA  LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.458  1.658 -0.200 1.90e-02 2.77e+03 1.11e+02
  bond model="   4" pdb=" N   LYS A  79 "
       model="   4" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.650 -0.192 1.90e-02 2.77e+03 1.03e+02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       69.84 -    89.18: 11
       89.18 -   108.52: 785
      108.52 -   127.85: 3231
      127.85 -   147.19: 46
      147.19 -   166.53: 4
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   4" pdb=" C   ILE A  78 "
        model="   4" pdb=" N   LYS A  79 "
        model="   4" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  159.17  -37.47 1.80e+00 3.09e-01 4.33e+02
  angle model="   4" pdb=" CA  ILE A  78 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" HB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00  166.53  -57.53 3.00e+00 1.11e-01 3.68e+02
  angle model="   4" pdb=" CA  ILE A  78 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CG1 ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.40   80.69   29.71 1.70e+00 3.46e-01 3.05e+02
  angle model="   4" pdb=" CA  ILE A  78 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CG2 ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.50   83.41   27.09 1.70e+00 3.46e-01 2.54e+02
  angle model="   4" pdb=" CG1 ILE A  78 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CG2 ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.70  156.22  -45.52 3.00e+00 1.11e-01 2.30e+02
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.71: 922
       23.71 -    47.41: 64
       47.41 -    71.12: 18
       71.12 -    94.82: 6
       94.82 -   118.53: 3
  Dihedral angle restraints: 1013
    sinusoidal: 562
      harmonic: 451
  Sorted by residual:
  dihedral model="   4" pdb=" CA  LYS A  79 "
           model="   4" pdb=" C   LYS A  79 "
           model="   4" pdb=" N   GLY A  80 "
           model="   4" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   61.47  118.53     0      5.00e+00 4.00e-02 5.62e+02
  dihedral model="   4" pdb=" CA  THR A  92 "
           model="   4" pdb=" C   THR A  92 "
           model="   4" pdb=" N   LEU A  93 "
           model="   4" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -66.01 -113.99     0      5.00e+00 4.00e-02 5.20e+02
  dihedral model="   4" pdb=" CA  TYR A  89 "
           model="   4" pdb=" C   TYR A  89 "
           model="   4" pdb=" N   SER A  90 "
           model="   4" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -79.64 -100.36     0      5.00e+00 4.00e-02 4.03e+02
  ... (remaining 1010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.119: 161
       1.119 -    2.238: 1
       2.238 -    3.357: 1
       3.357 -    4.476: 4
       4.476 -    5.595: 9
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CA  ALA A 124 "
            model="   4" pdb=" N   ALA A 124 "
            model="   4" pdb=" C   ALA A 124 "
            model="   4" pdb=" CB  ALA A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48   -3.11    5.59 2.00e-01 2.50e+01 7.82e+02
  chirality model="   4" pdb=" CA  ILE A 131 "
            model="   4" pdb=" N   ILE A 131 "
            model="   4" pdb=" C   ILE A 131 "
            model="   4" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -2.93    5.36 2.00e-01 2.50e+01 7.19e+02
  chirality model="   4" pdb=" CA  LYS A  79 "
            model="   4" pdb=" N   LYS A  79 "
            model="   4" pdb=" C   LYS A  79 "
            model="   4" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.65    5.16 2.00e-01 2.50e+01 6.66e+02
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  91 "    0.235 2.00e-02 2.50e+03   9.12e-02 2.49e+02
        model="   4" pdb=" CG  TYR A  91 "   -0.042 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  91 "   -0.068 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  91 "   -0.049 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  91 "   -0.013 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  91 "    0.044 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  91 "    0.074 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  91 "   -0.138 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  91 "   -0.078 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  91 "    0.047 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  91 "   -0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  89 "    0.158 2.00e-02 2.50e+03   6.83e-02 1.40e+02
        model="   4" pdb=" CG  TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  89 "   -0.031 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  89 "   -0.035 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  89 "   -0.020 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  89 "   -0.018 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  89 "    0.021 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  89 "    0.127 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  89 "   -0.060 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  89 "   -0.072 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  89 "   -0.041 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  89 "   -0.032 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  50 "   -0.123 2.00e-02 2.50e+03   5.18e-02 8.05e+01
        model="   4" pdb=" CG  TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  50 "    0.029 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  50 "   -0.098 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  50 "    0.051 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  50 "    0.034 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  50 "    0.035 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.02: 71
        2.02 -     2.67: 3075
        2.67 -     3.31: 6794
        3.31 -     3.96: 8375
        3.96 -     4.60: 12199
  Nonbonded interactions: 30514
  Sorted by model distance:
  nonbonded model="   4" pdb=" H   LYS A  79 "
            model="   4" pdb=" H   TYR A  81 "
     model   vdw
     1.378 2.100
  nonbonded model="   4" pdb=" H   ASP A 116 "
            model="   4" pdb=" HD3 PRO A 117 "
     model   vdw
     1.567 2.270
  nonbonded model="   4" pdb=" HA  ILE A  77 "
            model="   4" pdb="HG12 ILE A  78 "
     model   vdw
     1.645 2.440
  nonbonded model="   4" pdb=" H   LYS A  85 "
            model="   4" pdb=" HB2 SER A  90 "
     model   vdw
     1.654 2.270
  nonbonded model="   4" pdb="HG21 ILE A  78 "
            model="   4" pdb=" HA3 GLY A  94 "
     model   vdw
     1.658 2.440
  ... (remaining 30509 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CB  SER A  90 "
        model="   1" pdb=" CB  SER A  98 "
        model="   1" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 1.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.21, per 1000 atoms: 0.55
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (46.532, 56.323, 72.251, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 47
        1.23 -     1.43: 426
        1.43 -     1.62: 657
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   6" pdb=" CA  GLY A 121 "
       model="   6" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.709 -0.193 1.80e-02 3.09e+03 1.15e+02
  bond model="   6" pdb=" N   ILE A 122 "
       model="   6" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.639 -0.181 1.90e-02 2.77e+03 9.04e+01
  bond model="   6" pdb=" N   VAL A 126 "
       model="   6" pdb=" CA  VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.601 -0.143 1.90e-02 2.77e+03 5.70e+01
  bond model="   6" pdb=" C   GLY A 121 "
       model="   6" pdb=" N   ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.329  1.434 -0.105 1.40e-02 5.10e+03 5.64e+01
  bond model="   6" pdb=" N   ARG A 127 "
       model="   6" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.589 -0.131 1.90e-02 2.77e+03 4.78e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       78.70 -    91.72: 5
       91.72 -   104.75: 92
      104.75 -   117.77: 2990
      117.77 -   130.79: 983
      130.79 -   143.81: 9
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   6" pdb=" N   MET A 128 "
        model="   6" pdb=" CA  MET A 128 "
        model="   6" pdb=" C   MET A 128 "
      ideal   model   delta    sigma   weight residual
     111.00   78.70   32.30 2.80e+00 1.28e-01 1.33e+02
  angle model="   6" pdb=" C   MET A 128 "
        model="   6" pdb=" CA  MET A 128 "
        model="   6" pdb=" CB  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.10  131.93  -21.83 1.90e+00 2.77e-01 1.32e+02
  angle model="   6" pdb=" N   MET A 128 "
        model="   6" pdb=" CA  MET A 128 "
        model="   6" pdb=" HA  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.00  143.81  -33.81 3.00e+00 1.11e-01 1.27e+02
  angle model="   6" pdb=" C   GLY A 121 "
        model="   6" pdb=" N   ILE A 122 "
        model="   6" pdb=" CA  ILE A 122 "
      ideal   model   delta    sigma   weight residual
     121.70  138.99  -17.29 1.80e+00 3.09e-01 9.23e+01
  angle model="   6" pdb=" N   THR A  92 "
        model="   6" pdb=" CA  THR A  92 "
        model="   6" pdb=" HA  THR A  92 "
      ideal   model   delta    sigma   weight residual
     110.00   81.48   28.52 3.00e+00 1.11e-01 9.04e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.39: 938
       22.39 -    44.78: 65
       44.78 -    67.16: 13
       67.16 -    89.55: 5
       89.55 -   111.94: 4
  Dihedral angle restraints: 1025
    sinusoidal: 562
      harmonic: 463
  Sorted by residual:
  dihedral model="   6" pdb=" CA  VAL A 126 "
           model="   6" pdb=" C   VAL A 126 "
           model="   6" pdb=" N   ARG A 127 "
           model="   6" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   68.06  111.94     0      5.00e+00 4.00e-02 5.01e+02
  dihedral model="   6" pdb=" CA  TYR A  91 "
           model="   6" pdb=" C   TYR A  91 "
           model="   6" pdb=" N   THR A  92 "
           model="   6" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -68.39 -111.61     0      5.00e+00 4.00e-02 4.98e+02
  dihedral model="   6" pdb=" CA  MET A 128 "
           model="   6" pdb=" C   MET A 128 "
           model="   6" pdb=" N   ARG A 129 "
           model="   6" pdb=" CA  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   81.25   98.75     0      5.00e+00 4.00e-02 3.90e+02
  ... (remaining 1022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.044: 169
       1.044 -    2.087: 2
       2.087 -    3.130: 0
       3.130 -    4.173: 2
       4.173 -    5.216: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CB  THR A  92 "
            model="   6" pdb=" CA  THR A  92 "
            model="   6" pdb=" OG1 THR A  92 "
            model="   6" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.66    5.22 2.00e-01 2.50e+01 6.80e+02
  chirality model="   6" pdb=" CA  MET A 128 "
            model="   6" pdb=" N   MET A 128 "
            model="   6" pdb=" C   MET A 128 "
            model="   6" pdb=" CB  MET A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.69    5.20 2.00e-01 2.50e+01 6.75e+02
  chirality model="   6" pdb=" CA  LYS A  79 "
            model="   6" pdb=" N   LYS A  79 "
            model="   6" pdb=" C   LYS A  79 "
            model="   6" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.98    4.49 2.00e-01 2.50e+01 5.04e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  91 "   -0.099 2.00e-02 2.50e+03   6.78e-02 1.38e+02
        model="   6" pdb=" CG  TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  91 "    0.028 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  91 "    0.021 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  91 "    0.047 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  91 "   -0.162 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  91 "    0.055 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  91 "   -0.022 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  91 "    0.027 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  91 "    0.106 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  12 "    0.140 2.00e-02 2.50e+03   6.04e-02 1.09e+02
        model="   6" pdb=" CG  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  12 "   -0.030 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  12 "    0.120 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  12 "   -0.045 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  12 "   -0.054 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  12 "   -0.038 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  12 "   -0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  50 "    0.100 2.00e-02 2.50e+03   4.26e-02 5.46e+01
        model="   6" pdb=" CG  TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  50 "    0.086 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  50 "   -0.025 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  50 "   -0.039 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.13 -     1.83: 8
        1.83 -     2.52: 1727
        2.52 -     3.21: 6849
        3.21 -     3.91: 8163
        3.91 -     4.60: 12482
  Nonbonded interactions: 29229
  Sorted by model distance:
  nonbonded model="   6" pdb=" HA  VAL A 126 "
            model="   6" pdb=" H   MET A 128 "
     model   vdw
     1.133 2.270
  nonbonded model="   6" pdb=" HA  LYS A 125 "
            model="   6" pdb=" H   ARG A 127 "
     model   vdw
     1.631 2.270
  nonbonded model="   6" pdb=" HA  ALA A 124 "
            model="   6" pdb=" H   VAL A 126 "
     model   vdw
     1.643 2.270
  nonbonded model="   6" pdb="HG22 ILE A  77 "
            model="   6" pdb=" H   ILE A  78 "
     model   vdw
     1.668 2.270
  nonbonded model="   6" pdb=" H   THR A  92 "
            model="   6" pdb=" HA  THR A  92 "
     model   vdw
     1.685 1.816
  ... (remaining 29224 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1105
        1.04 -     1.23: 61
        1.23 -     1.43: 417
        1.43 -     1.62: 652
        1.62 -     1.82: 6
  Bond restraints: 2241
  Sorted by residual:
  bond model="   1" pdb=" N   LYS A  79 "
       model="   1" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.623 -0.165 1.90e-02 2.77e+03 7.57e+01
  bond model="   1" pdb=" CA  ILE A  78 "
       model="   1" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.693 -0.168 2.10e-02 2.27e+03 6.43e+01
  bond model="   1" pdb=" N   GLY A  80 "
       model="   1" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.557 -0.106 1.60e-02 3.91e+03 4.38e+01
  bond model="   1" pdb=" N   ILE A  77 "
       model="   1" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.580 -0.122 1.90e-02 2.77e+03 4.13e+01
  bond model="   1" pdb=" C   ILE A  78 "
       model="   1" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.392 -0.063 1.40e-02 5.10e+03 2.00e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       71.96 -    91.46: 8
       91.46 -   110.96: 2323
      110.96 -   130.46: 1735
      130.46 -   149.96: 10
      149.96 -   169.46: 1
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   1" pdb=" C   ILE A  78 "
        model="   1" pdb=" N   LYS A  79 "
        model="   1" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  169.46  -47.76 1.80e+00 3.09e-01 7.04e+02
  angle model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CA  ILE A  51 "
        model="   1" pdb=" HA  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   71.96   37.04 3.00e+00 1.11e-01 1.52e+02
  angle model="   1" pdb=" N   LYS A  79 "
        model="   1" pdb=" CA  LYS A  79 "
        model="   1" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.50  131.35  -20.85 1.70e+00 3.46e-01 1.50e+02
  angle model="   1" pdb=" C   ILE A  77 "
        model="   1" pdb=" CA  ILE A  77 "
        model="   1" pdb=" HA  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     109.00   73.71   35.29 3.00e+00 1.11e-01 1.38e+02
  angle model="   1" pdb=" N   SER A  76 "
        model="   1" pdb=" CA  SER A  76 "
        model="   1" pdb=" CB  SER A  76 "
      ideal   model   delta    sigma   weight residual
     110.50   90.68   19.82 1.70e+00 3.46e-01 1.36e+02
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.22: 947
       20.22 -    40.43: 51
       40.43 -    60.65: 16
       60.65 -    80.87: 5
       80.87 -   101.08: 3
  Dihedral angle restraints: 1022
    sinusoidal: 561
      harmonic: 461
  Sorted by residual:
  dihedral model="   1" pdb=" CA  ILE A  77 "
           model="   1" pdb=" C   ILE A  77 "
           model="   1" pdb=" N   ILE A  78 "
           model="   1" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   78.92  101.08     0      5.00e+00 4.00e-02 4.09e+02
  dihedral model="   1" pdb=" CA  SER A  90 "
           model="   1" pdb=" C   SER A  90 "
           model="   1" pdb=" N   TYR A  91 "
           model="   1" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   90.72   89.28     0      5.00e+00 4.00e-02 3.19e+02
  dihedral model="   1" pdb=" CA  LYS A  79 "
           model="   1" pdb=" C   LYS A  79 "
           model="   1" pdb=" N   GLY A  80 "
           model="   1" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  102.22   77.78     0      5.00e+00 4.00e-02 2.42e+02
  ... (remaining 1019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.058: 168
       1.058 -    2.116: 2
       2.116 -    3.174: 1
       3.174 -    4.232: 0
       4.232 -    5.290: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  LYS A  79 "
            model="   1" pdb=" N   LYS A  79 "
            model="   1" pdb=" C   LYS A  79 "
            model="   1" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.78    5.29 2.00e-01 2.50e+01 7.00e+02
  chirality model="   1" pdb=" CB  ILE A  78 "
            model="   1" pdb=" CA  ILE A  78 "
            model="   1" pdb=" CG1 ILE A  78 "
            model="   1" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.64    5.28 2.00e-01 2.50e+01 6.97e+02
  chirality model="   1" pdb=" CA  SER A  98 "
            model="   1" pdb=" N   SER A  98 "
            model="   1" pdb=" C   SER A  98 "
            model="   1" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.54    5.05 2.00e-01 2.50e+01 6.38e+02
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  91 "   -0.171 2.00e-02 2.50e+03   7.48e-02 1.68e+02
        model="   1" pdb=" CG  TYR A  91 "    0.079 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  91 "    0.041 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  91 "    0.035 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  91 "    0.025 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  91 "    0.034 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  91 "    0.025 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  91 "   -0.155 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  91 "    0.026 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  91 "    0.008 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  91 "    0.039 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  PHE A  15 "    0.152 2.00e-02 2.50e+03   5.75e-02 9.93e+01
        model="   1" pdb=" CG  PHE A  15 "   -0.044 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 PHE A  15 "   -0.038 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 PHE A  15 "   -0.041 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  PHE A  15 "    0.023 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 PHE A  15 "   -0.060 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 PHE A  15 "   -0.066 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 PHE A  15 "    0.007 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 PHE A  15 "    0.012 2.00e-02 2.50e+03
        model="   1" pdb=" HZ  PHE A  15 "    0.055 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  89 "   -0.112 2.00e-02 2.50e+03   4.73e-02 6.70e+01
        model="   1" pdb=" CG  TYR A  89 "    0.011 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  89 "    0.017 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  89 "    0.036 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  89 "    0.016 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  89 "   -0.005 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  89 "   -0.011 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  89 "   -0.057 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  89 "    0.020 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  89 "    0.080 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  89 "    0.034 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  89 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.44 -     2.07: 69
        2.07 -     2.70: 3465
        2.70 -     3.33: 6644
        3.33 -     3.97: 8094
        3.97 -     4.60: 12062
  Nonbonded interactions: 30334
  Sorted by model distance:
  nonbonded model="   1" pdb=" HA  ILE A  77 "
            model="   1" pdb=" HA  LYS A  79 "
     model   vdw
     1.436 2.440
  nonbonded model="   1" pdb=" H   GLY A  87 "
            model="   1" pdb=" H   TYR A  89 "
     model   vdw
     1.552 2.100
  nonbonded model="   1" pdb=" HA  ILE A  51 "
            model="   1" pdb=" HB  ILE A  51 "
     model   vdw
     1.585 1.952
  nonbonded model="   1" pdb=" HB3 SER A  76 "
            model="   1" pdb=" HB2 LYS A  79 "
     model   vdw
     1.673 2.440
  nonbonded model="   1" pdb=" H   ASP A  95 "
            model="   1" pdb=" H   GLY A  96 "
     model   vdw
     1.737 2.100
  ... (remaining 30329 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  13" pdb=" CB  THR A  83 "
  Number of C-beta restraints generated:  262

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 102
        1.23 -     1.43: 370
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  10" pdb=" CD2 HIS A  43 "
       model="  10" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.374  1.406 -0.032 1.10e-02 8.26e+03 8.62e+00
  bond model="  10" pdb=" CD2 HIS A 139 "
       model="  10" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.66e+00
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.18e+00
  bond model="  10" pdb=" CD2 HIS A 135 "
       model="  10" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.14e+00
  bond model="  10" pdb=" CE1 HIS A 139 "
       model="  10" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.66e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.07 -   105.22: 71
      105.22 -   111.37: 2383
      111.37 -   117.52: 626
      117.52 -   123.67: 855
      123.67 -   129.83: 144
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  10" pdb=" CA  HIS A 135 "
        model="  10" pdb=" CB  HIS A 135 "
        model="  10" pdb=" CG  HIS A 135 "
      ideal   model   delta    sigma   weight residual
     113.80  118.85   -5.05 1.00e+00 1.00e+00 2.55e+01
  angle model="  10" pdb=" OE1 GLN A 100 "
        model="  10" pdb=" CD  GLN A 100 "
        model="  10" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  117.61    4.99 1.00e+00 1.00e+00 2.49e+01
  angle model="  10" pdb=" CA  THR A  82 "
        model="  10" pdb=" CB  THR A  82 "
        model="  10" pdb=" OG1 THR A  82 "
      ideal   model   delta    sigma   weight residual
     109.60  116.82   -7.22 1.50e+00 4.44e-01 2.32e+01
  angle model="  10" pdb=" C   GLY A 121 "
        model="  10" pdb=" N   ILE A 122 "
        model="  10" pdb=" CA  ILE A 122 "
      ideal   model   delta    sigma   weight residual
     121.70  129.83   -8.13 1.80e+00 3.09e-01 2.04e+01
  angle model="  10" pdb=" OE1 GLN A  28 "
        model="  10" pdb=" CD  GLN A  28 "
        model="  10" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.53    4.07 1.00e+00 1.00e+00 1.65e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 936
       17.79 -    35.59: 61
       35.59 -    53.38: 22
       53.38 -    71.17: 8
       71.17 -    88.96: 6
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  10" pdb=" CA  GLU A 133 "
           model="  10" pdb=" C   GLU A 133 "
           model="  10" pdb=" N   HIS A 134 "
           model="  10" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.95   39.05     0      5.00e+00 4.00e-02 6.10e+01
  dihedral model="  10" pdb=" CA  LEU A   2 "
           model="  10" pdb=" C   LEU A   2 "
           model="  10" pdb=" N   LEU A   3 "
           model="  10" pdb=" CA  LEU A   3 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.80  -31.20     0      5.00e+00 4.00e-02 3.89e+01
  dihedral model="  10" pdb=" CA  LEU A 119 "
           model="  10" pdb=" C   LEU A 119 "
           model="  10" pdb=" N   GLU A 120 "
           model="  10" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.91   25.09     0      5.00e+00 4.00e-02 2.52e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.081: 104
       0.081 -    0.160: 57
       0.160 -    0.240: 12
       0.240 -    0.319: 2
       0.319 -    0.398: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CA  LEU A   3 "
            model="  10" pdb=" N   LEU A   3 "
            model="  10" pdb=" C   LEU A   3 "
            model="  10" pdb=" CB  LEU A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.96e+00
  chirality model="  10" pdb=" CA  ARG A 127 "
            model="  10" pdb=" N   ARG A 127 "
            model="  10" pdb=" C   ARG A 127 "
            model="  10" pdb=" CB  ARG A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality model="  10" pdb=" CA  HIS A 137 "
            model="  10" pdb=" N   HIS A 137 "
            model="  10" pdb=" C   HIS A 137 "
            model="  10" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  89 "   -0.148 2.00e-02 2.50e+03   8.03e-02 1.94e+02
        model="  10" pdb=" CG  TYR A  89 "   -0.035 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  89 "    0.033 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  89 "    0.018 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  89 "    0.018 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  89 "    0.037 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  89 "   -0.046 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  89 "   -0.162 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  89 "    0.089 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  89 "    0.041 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  89 "    0.051 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  89 "    0.104 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  12 "   -0.155 2.00e-02 2.50e+03   6.96e-02 1.45e+02
        model="  10" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  12 "    0.036 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  12 "    0.027 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  12 "    0.022 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  12 "    0.030 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  12 "   -0.147 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  12 "    0.069 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  12 "    0.041 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  12 "    0.046 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  81 "    0.094 2.00e-02 2.50e+03   4.99e-02 7.48e+01
        model="  10" pdb=" CG  TYR A  81 "    0.010 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  81 "   -0.004 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  81 "   -0.039 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  81 "   -0.019 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  81 "    0.016 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  81 "    0.021 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  81 "    0.040 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  81 "   -0.108 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  81 "   -0.054 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  81 "    0.048 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 386
        2.31 -     2.88: 5076
        2.88 -     3.45: 5233
        3.45 -     4.03: 6774
        4.03 -     4.60: 10079
  Nonbonded interactions: 27548
  Sorted by model distance:
  nonbonded model="  10" pdb=" H   THR A  82 "
            model="  10" pdb=" HG1 THR A  82 "
     model   vdw
     1.734 2.100
  nonbonded model="  10" pdb=" OE1 GLU A 123 "
            model="  10" pdb=" HZ2 LYS A 125 "
     model   vdw
     1.795 1.850
  nonbonded model="  10" pdb=" OD2 ASP A  36 "
            model="  10" pdb=" HZ1 LYS A  40 "
     model   vdw
     1.809 1.850
  nonbonded model="  10" pdb="HG22 VAL A  41 "
            model="  10" pdb=" HB3 PRO A 114 "
     model   vdw
     1.848 2.440
  nonbonded model="  10" pdb=" OE2 GLU A  32 "
            model="  10" pdb=" HG1 THR A  82 "
     model   vdw
     1.849 1.850
  ... (remaining 27543 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 74
        1.23 -     1.43: 398
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" CZ  ARG A  21 "
       model="  13" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.24e+00
  bond model="  13" pdb=" CD2 HIS A 138 "
       model="  13" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.12e+00
  bond model="  13" pdb=" CB  THR A  82 "
       model="  13" pdb=" OG1 THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.433  1.394  0.039 1.60e-02 3.91e+03 5.97e+00
  bond model="  13" pdb=" CD2 HIS A 134 "
       model="  13" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.93e+00
  bond model="  13" pdb=" CD2 HIS A 136 "
       model="  13" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.81e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.14 -   105.98: 128
      105.98 -   112.81: 2609
      112.81 -   119.65: 528
      119.65 -   126.49: 792
      126.49 -   133.33: 22
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" C   THR A  83 "
        model="  13" pdb=" N   GLU A  84 "
        model="  13" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  133.33  -11.63 1.80e+00 3.09e-01 4.17e+01
  angle model="  13" pdb=" C   THR A  82 "
        model="  13" pdb=" N   THR A  83 "
        model="  13" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  132.35  -10.65 1.80e+00 3.09e-01 3.50e+01
  angle model="  13" pdb=" C   VAL A 112 "
        model="  13" pdb=" N   LYS A 113 "
        model="  13" pdb=" CA  LYS A 113 "
      ideal   model   delta    sigma   weight residual
     121.70  129.51   -7.81 1.80e+00 3.09e-01 1.88e+01
  angle model="  13" pdb=" OE1 GLN A 100 "
        model="  13" pdb=" CD  GLN A 100 "
        model="  13" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.39    4.21 1.00e+00 1.00e+00 1.77e+01
  angle model="  13" pdb=" OE1 GLN A  66 "
        model="  13" pdb=" CD  GLN A  66 "
        model="  13" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.44    4.16 1.00e+00 1.00e+00 1.73e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.03: 960
       19.03 -    38.07: 42
       38.07 -    57.10: 16
       57.10 -    76.14: 6
       76.14 -    95.17: 7
  Dihedral angle restraints: 1031
    sinusoidal: 562
      harmonic: 469
  Sorted by residual:
  dihedral model="  13" pdb=" CA  ILE A  86 "
           model="  13" pdb=" C   ILE A  86 "
           model="  13" pdb=" N   GLY A  87 "
           model="  13" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -84.83  -95.17     0      5.00e+00 4.00e-02 3.62e+02
  dihedral model="  13" pdb=" CA  HIS A 138 "
           model="  13" pdb=" C   HIS A 138 "
           model="  13" pdb=" N   HIS A 139 "
           model="  13" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.96   22.04     0      5.00e+00 4.00e-02 1.94e+01
  dihedral model="  13" pdb=" CA  THR A  83 "
           model="  13" pdb=" C   THR A  83 "
           model="  13" pdb=" N   GLU A  84 "
           model="  13" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.12   21.88     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 1028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.868: 175
       0.868 -    1.737: 0
       1.737 -    2.605: 0
       2.605 -    3.473: 0
       3.473 -    4.341: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  THR A  83 "
            model="  13" pdb=" N   THR A  83 "
            model="  13" pdb=" C   THR A  83 "
            model="  13" pdb=" CB  THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -1.82    4.34 2.00e-01 2.50e+01 4.71e+02
  chirality model="  13" pdb=" CA  GLU A  84 "
            model="  13" pdb=" N   GLU A  84 "
            model="  13" pdb=" C   GLU A  84 "
            model="  13" pdb=" CB  GLU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality model="  13" pdb=" CA  HIS A 138 "
            model="  13" pdb=" N   HIS A 138 "
            model="  13" pdb=" C   HIS A 138 "
            model="  13" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.82e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A 111 "    0.250 2.00e-02 2.50e+03   1.04e-01 3.22e+02
        model="  13" pdb=" CG  TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A 111 "   -0.058 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A 111 "   -0.050 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A 111 "   -0.025 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A 111 "   -0.033 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A 111 "    0.191 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A 111 "   -0.105 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A 111 "   -0.080 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A 111 "   -0.033 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A 111 "   -0.056 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  HIS A 138 "    0.106 2.00e-02 2.50e+03   6.34e-02 8.05e+01
        model="  13" pdb=" CG  HIS A 138 "   -0.082 2.00e-02 2.50e+03
        model="  13" pdb=" ND1 HIS A 138 "   -0.096 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 HIS A 138 "   -0.019 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 HIS A 138 "    0.010 2.00e-02 2.50e+03
        model="  13" pdb=" NE2 HIS A 138 "    0.033 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 HIS A 138 "   -0.012 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 HIS A 138 "    0.059 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  HIS A 139 "   -0.061 2.00e-02 2.50e+03   4.85e-02 4.70e+01
        model="  13" pdb=" CG  HIS A 139 "    0.086 2.00e-02 2.50e+03
        model="  13" pdb=" ND1 HIS A 139 "    0.032 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 HIS A 139 "    0.014 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 HIS A 139 "   -0.008 2.00e-02 2.50e+03
        model="  13" pdb=" NE2 HIS A 139 "    0.036 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 HIS A 139 "   -0.041 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 HIS A 139 "   -0.059 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 380
        2.31 -     2.88: 5015
        2.88 -     3.45: 5338
        3.45 -     4.03: 6856
        4.03 -     4.60: 10438
  Nonbonded interactions: 28027
  Sorted by model distance:
  nonbonded model="  13" pdb=" HB  THR A  83 "
            model="  13" pdb=" H   GLU A  84 "
     model   vdw
     1.734 2.270
  nonbonded model="  13" pdb=" OD1 ASP A  44 "
            model="  13" pdb=" HG  SER A  46 "
     model   vdw
     1.788 1.850
  nonbonded model="  13" pdb=" HZ1 LYS A 101 "
            model="  13" pdb=" OXT HIS A 139 "
     model   vdw
     1.838 1.850
  nonbonded model="  13" pdb=" HZ2 LYS A  10 "
            model="  13" pdb=" OD1 ASP A  23 "
     model   vdw
     1.844 1.850
  nonbonded model="  13" pdb=" OE1 GLU A  24 "
            model="  13" pdb=" HZ1 LYS A  27 "
     model   vdw
     1.848 1.850
  ... (remaining 28022 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.09 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.03 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 463
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   8" pdb=" N   MET A   1 "
       model="   8" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.40e+00
  bond model="   8" pdb=" CZ  ARG A  58 "
       model="   8" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.327 -0.004 1.40e-02 5.10e+03 6.82e-02
  bond model="   8" pdb=" CZ  ARG A  58 "
       model="   8" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 6.34e-02
  bond model="   8" pdb=" NE  ARG A  21 "
       model="   8" pdb=" CZ  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 5.42e-02
  bond model="   8" pdb=" CZ  ARG A 127 "
       model="   8" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.23e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.88 -   106.88: 65
      106.88 -   112.88: 2720
      112.88 -   118.88: 426
      118.88 -   124.88: 824
      124.88 -   130.88: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   8" pdb=" CB  PRO A  52 "
        model="   8" pdb=" CA  PRO A  52 "
        model="   8" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.84   -4.84 3.00e+00 1.11e-01 2.60e+00
  angle model="   8" pdb=" CB  PRO A  54 "
        model="   8" pdb=" CA  PRO A  54 "
        model="   8" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   8" pdb=" CB  PRO A 102 "
        model="   8" pdb=" CA  PRO A 102 "
        model="   8" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   8" pdb=" CB  PRO A 114 "
        model="   8" pdb=" CA  PRO A 114 "
        model="   8" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   8" pdb=" CB  PRO A  22 "
        model="   8" pdb=" CA  PRO A  22 "
        model="   8" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.78   -4.78 3.00e+00 1.11e-01 2.54e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.70: 867
       15.70 -    31.41: 75
       31.41 -    47.11: 59
       47.11 -    62.81: 28
       62.81 -    78.51: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   8" pdb=" N   LEU A   2 "
           model="   8" pdb=" CA  LEU A   2 "
           model="   8" pdb=" CB  LEU A   2 "
           model="   8" pdb=" CG  LEU A   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.11  -59.89     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   8" pdb=" CA  GLU A  75 "
           model="   8" pdb=" CB  GLU A  75 "
           model="   8" pdb=" CG  GLU A  75 "
           model="   8" pdb=" CD  GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.37  -59.37     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   8" pdb=" N   GLU A 123 "
           model="   8" pdb=" CA  GLU A 123 "
           model="   8" pdb=" CB  GLU A 123 "
           model="   8" pdb=" CG  GLU A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.80  -59.20     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.019: 112
       0.019 -    0.038: 41
       0.038 -    0.057: 4
       0.057 -    0.076: 0
       0.076 -    0.094: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  ILE A  77 "
            model="   8" pdb=" N   ILE A  77 "
            model="   8" pdb=" C   ILE A  77 "
            model="   8" pdb=" CB  ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.23e-01
  chirality model="   8" pdb=" CA  ILE A 131 "
            model="   8" pdb=" N   ILE A 131 "
            model="   8" pdb=" C   ILE A 131 "
            model="   8" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.21e-01
  chirality model="   8" pdb=" CA  ILE A  51 "
            model="   8" pdb=" N   ILE A  51 "
            model="   8" pdb=" C   ILE A  51 "
            model="   8" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.15e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  50 "    0.000 2.00e-02 2.50e+03   1.28e-03 4.90e-02
        model="   8" pdb=" CG  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  50 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  68 "    0.001 2.00e-02 2.50e+03   9.33e-04 2.61e-02
        model="   8" pdb=" CG  TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  68 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  68 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  89 "    0.000 2.00e-02 2.50e+03   8.70e-04 2.27e-02
        model="   8" pdb=" CG  TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  89 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.13: 120
        2.13 -     2.75: 4237
        2.75 -     3.37: 5871
        3.37 -     3.98: 7036
        3.98 -     4.60: 10852
  Nonbonded interactions: 28116
  Sorted by model distance:
  nonbonded model="   8" pdb="HD23 LEU A   9 "
            model="   8" pdb="HD22 LEU A  26 "
     model   vdw
     1.517 2.440
  nonbonded model="   8" pdb="HD11 LEU A  93 "
            model="   8" pdb="HD13 LEU A  99 "
     model   vdw
     1.608 2.440
  nonbonded model="   8" pdb="HG23 ILE A  37 "
            model="   8" pdb="HD13 ILE A 108 "
     model   vdw
     1.684 2.440
  nonbonded model="   8" pdb="HG12 VAL A  41 "
            model="   8" pdb=" HA  VAL A 112 "
     model   vdw
     1.708 2.440
  nonbonded model="   8" pdb="HD12 LEU A   2 "
            model="   8" pdb="HG23 ILE A   4 "
     model   vdw
     1.745 2.440
  ... (remaining 28111 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.42e+00
  bond model="   9" pdb=" NE  ARG A 129 "
       model="   9" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 7.02e-02
  bond model="   9" pdb=" NE  ARG A 127 "
       model="   9" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 6.83e-02
  bond model="   9" pdb=" CZ  ARG A 127 "
       model="   9" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 6.12e-02
  bond model="   9" pdb=" CZ  ARG A  21 "
       model="   9" pdb=" NH1 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.39e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.87 -   106.88: 67
      106.88 -   112.89: 2718
      112.89 -   118.89: 426
      118.89 -   124.90: 824
      124.90 -   130.91: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A   6 "
        model="   9" pdb=" CA  PRO A   6 "
        model="   9" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   9" pdb=" CB  PRO A  52 "
        model="   9" pdb=" CA  PRO A  52 "
        model="   9" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   9" pdb=" CB  PRO A  22 "
        model="   9" pdb=" CA  PRO A  22 "
        model="   9" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   9" pdb=" CB  PRO A 114 "
        model="   9" pdb=" CA  PRO A 114 "
        model="   9" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   9" pdb=" CB  PRO A  54 "
        model="   9" pdb=" CA  PRO A  54 "
        model="   9" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 881
       17.66 -    35.33: 75
       35.33 -    52.99: 51
       52.99 -    70.65: 20
       70.65 -    88.32: 5
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CB  GLU A 120 "
           model="   9" pdb=" CG  GLU A 120 "
           model="   9" pdb=" CD  GLU A 120 "
           model="   9" pdb=" OE1 GLU A 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.32  -88.32     1      3.00e+01 1.11e-03 1.04e+01
  dihedral model="   9" pdb=" CB  GLU A  24 "
           model="   9" pdb=" CG  GLU A  24 "
           model="   9" pdb=" CD  GLU A  24 "
           model="   9" pdb=" OE1 GLU A  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.27  -88.27     1      3.00e+01 1.11e-03 1.03e+01
  dihedral model="   9" pdb=" CA  ASP A 116 "
           model="   9" pdb=" CB  ASP A 116 "
           model="   9" pdb=" CG  ASP A 116 "
           model="   9" pdb=" OD1 ASP A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.26   53.26     1      2.00e+01 2.50e-03 9.64e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 100
       0.019 -    0.038: 54
       0.038 -    0.057: 3
       0.057 -    0.076: 0
       0.076 -    0.095: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A 122 "
            model="   9" pdb=" N   ILE A 122 "
            model="   9" pdb=" C   ILE A 122 "
            model="   9" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.25e-01
  chirality model="   9" pdb=" CA  ILE A 131 "
            model="   9" pdb=" N   ILE A 131 "
            model="   9" pdb=" C   ILE A 131 "
            model="   9" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.18e-01
  chirality model="   9" pdb=" CA  ILE A  71 "
            model="   9" pdb=" N   ILE A  71 "
            model="   9" pdb=" C   ILE A  71 "
            model="   9" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  15 "   -0.001 2.00e-02 2.50e+03   1.23e-03 4.54e-02
        model="   9" pdb=" CG  PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  15 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  15 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  15 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  45 "    0.000 2.00e-02 2.50e+03   1.00e-03 3.01e-02
        model="   9" pdb=" CG  PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  45 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  68 "   -0.000 2.00e-02 2.50e+03   9.10e-04 2.48e-02
        model="   9" pdb=" CG  TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  68 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 155
        2.15 -     2.76: 4427
        2.76 -     3.38: 5842
        3.38 -     3.99: 7210
        3.99 -     4.60: 10785
  Nonbonded interactions: 28419
  Sorted by model distance:
  nonbonded model="   9" pdb="HD12 ILE A  37 "
            model="   9" pdb="HD12 LEU A  61 "
     model   vdw
     1.541 2.440
  nonbonded model="   9" pdb="HD11 LEU A  93 "
            model="   9" pdb="HD13 LEU A  99 "
     model   vdw
     1.572 2.440
  nonbonded model="   9" pdb="HG13 VAL A  41 "
            model="   9" pdb="HD12 ILE A 108 "
     model   vdw
     1.591 2.440
  nonbonded model="   9" pdb="HD13 LEU A   3 "
            model="   9" pdb="HD22 LEU A  53 "
     model   vdw
     1.640 2.440
  nonbonded model="   9" pdb=" H2  MET A   1 "
            model="   9" pdb="HD22 LEU A  31 "
     model   vdw
     1.703 2.270
  ... (remaining 28414 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 69
        1.23 -     1.42: 403
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  15" pdb=" CD2 HIS A 139 "
       model="  15" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.66e+00
  bond model="  15" pdb=" CD2 HIS A  43 "
       model="  15" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.31e+00
  bond model="  15" pdb=" CZ  ARG A  21 "
       model="  15" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.57e+00
  bond model="  15" pdb=" CE1 HIS A 136 "
       model="  15" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.84e+00
  bond model="  15" pdb=" CZ  ARG A  58 "
       model="  15" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.76e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.70 -   104.88: 52
      104.88 -   111.07: 2340
      111.07 -   117.25: 662
      117.25 -   123.44: 862
      123.44 -   129.62: 163
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  15" pdb=" CA  PHE A  67 "
        model="  15" pdb=" CB  PHE A  67 "
        model="  15" pdb=" CG  PHE A  67 "
      ideal   model   delta    sigma   weight residual
     113.80  107.38    6.42 1.00e+00 1.00e+00 4.12e+01
  angle model="  15" pdb=" OE1 GLN A  66 "
        model="  15" pdb=" CD  GLN A  66 "
        model="  15" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.85    4.75 1.00e+00 1.00e+00 2.26e+01
  angle model="  15" pdb=" OE1 GLN A 100 "
        model="  15" pdb=" CD  GLN A 100 "
        model="  15" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.27    4.33 1.00e+00 1.00e+00 1.87e+01
  angle model="  15" pdb=" OE1 GLN A  28 "
        model="  15" pdb=" CD  GLN A  28 "
        model="  15" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.35    4.25 1.00e+00 1.00e+00 1.80e+01
  angle model="  15" pdb=" CB  HIS A 138 "
        model="  15" pdb=" CG  HIS A 138 "
        model="  15" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  126.28    4.92 1.30e+00 5.92e-01 1.43e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 934
       16.85 -    33.69: 62
       33.69 -    50.54: 22
       50.54 -    67.38: 13
       67.38 -    84.23: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  15" pdb=" CA  TYR A  81 "
           model="  15" pdb=" C   TYR A  81 "
           model="  15" pdb=" N   THR A  82 "
           model="  15" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.83   22.17     0      5.00e+00 4.00e-02 1.97e+01
  dihedral model="  15" pdb=" CA  GLY A 121 "
           model="  15" pdb=" C   GLY A 121 "
           model="  15" pdb=" N   ILE A 122 "
           model="  15" pdb=" CA  ILE A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.40   20.60     0      5.00e+00 4.00e-02 1.70e+01
  dihedral model="  15" pdb=" CA  GLU A 120 "
           model="  15" pdb=" C   GLU A 120 "
           model="  15" pdb=" N   GLY A 121 "
           model="  15" pdb=" CA  GLY A 121 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.41   20.59     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 73
       0.049 -    0.098: 54
       0.098 -    0.146: 30
       0.146 -    0.195: 14
       0.195 -    0.244: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  15" pdb=" CA  TYR A  81 "
            model="  15" pdb=" N   TYR A  81 "
            model="  15" pdb=" C   TYR A  81 "
            model="  15" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality model="  15" pdb=" CA  TYR A 111 "
            model="  15" pdb=" N   TYR A 111 "
            model="  15" pdb=" C   TYR A 111 "
            model="  15" pdb=" CB  TYR A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality model="  15" pdb=" CB  ILE A  71 "
            model="  15" pdb=" CA  ILE A  71 "
            model="  15" pdb=" CG1 ILE A  71 "
            model="  15" pdb=" CG2 ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  15" pdb=" CB  PHE A  67 "    0.418 2.00e-02 2.50e+03   1.60e-01 7.72e+02
        model="  15" pdb=" CG  PHE A  67 "   -0.073 2.00e-02 2.50e+03
        model="  15" pdb=" CD1 PHE A  67 "   -0.107 2.00e-02 2.50e+03
        model="  15" pdb=" CD2 PHE A  67 "   -0.098 2.00e-02 2.50e+03
        model="  15" pdb=" CE1 PHE A  67 "   -0.008 2.00e-02 2.50e+03
        model="  15" pdb=" CE2 PHE A  67 "   -0.016 2.00e-02 2.50e+03
        model="  15" pdb=" CZ  PHE A  67 "    0.074 2.00e-02 2.50e+03
        model="  15" pdb=" HD1 PHE A  67 "   -0.193 2.00e-02 2.50e+03
        model="  15" pdb=" HD2 PHE A  67 "   -0.169 2.00e-02 2.50e+03
        model="  15" pdb=" HE1 PHE A  67 "    0.004 2.00e-02 2.50e+03
        model="  15" pdb=" HE2 PHE A  67 "   -0.020 2.00e-02 2.50e+03
        model="  15" pdb=" HZ  PHE A  67 "    0.189 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  15" pdb=" CB  TYR A  12 "   -0.248 2.00e-02 2.50e+03   1.15e-01 3.93e+02
        model="  15" pdb=" CG  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="  15" pdb=" CD1 TYR A  12 "    0.050 2.00e-02 2.50e+03
        model="  15" pdb=" CD2 TYR A  12 "    0.048 2.00e-02 2.50e+03
        model="  15" pdb=" CE1 TYR A  12 "    0.041 2.00e-02 2.50e+03
        model="  15" pdb=" CE2 TYR A  12 "    0.044 2.00e-02 2.50e+03
        model="  15" pdb=" CZ  TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="  15" pdb=" OH  TYR A  12 "   -0.244 2.00e-02 2.50e+03
        model="  15" pdb=" HD1 TYR A  12 "    0.092 2.00e-02 2.50e+03
        model="  15" pdb=" HD2 TYR A  12 "    0.085 2.00e-02 2.50e+03
        model="  15" pdb=" HE1 TYR A  12 "    0.074 2.00e-02 2.50e+03
        model="  15" pdb=" HE2 TYR A  12 "    0.082 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  15" pdb=" CB  TYR A  91 "   -0.258 2.00e-02 2.50e+03   1.09e-01 3.59e+02
        model="  15" pdb=" CG  TYR A  91 "    0.023 2.00e-02 2.50e+03
        model="  15" pdb=" CD1 TYR A  91 "    0.049 2.00e-02 2.50e+03
        model="  15" pdb=" CD2 TYR A  91 "    0.059 2.00e-02 2.50e+03
        model="  15" pdb=" CE1 TYR A  91 "    0.037 2.00e-02 2.50e+03
        model="  15" pdb=" CE2 TYR A  91 "    0.028 2.00e-02 2.50e+03
        model="  15" pdb=" CZ  TYR A  91 "   -0.036 2.00e-02 2.50e+03
        model="  15" pdb=" OH  TYR A  91 "   -0.207 2.00e-02 2.50e+03
        model="  15" pdb=" HD1 TYR A  91 "    0.074 2.00e-02 2.50e+03
        model="  15" pdb=" HD2 TYR A  91 "    0.103 2.00e-02 2.50e+03
        model="  15" pdb=" HE1 TYR A  91 "    0.077 2.00e-02 2.50e+03
        model="  15" pdb=" HE2 TYR A  91 "    0.050 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 379
        2.30 -     2.88: 5208
        2.88 -     3.45: 5449
        3.45 -     4.03: 7033
        4.03 -     4.60: 10648
  Nonbonded interactions: 28717
  Sorted by model distance:
  nonbonded model="  15" pdb=" HZ1 LYS A  10 "
            model="  15" pdb=" OD1 ASP A  23 "
     model   vdw
     1.727 1.850
  nonbonded model="  15" pdb=" HZ3 LYS A  63 "
            model="  15" pdb=" HB2 PRO A 102 "
     model   vdw
     1.729 2.270
  nonbonded model="  15" pdb=" OE2 GLU A  24 "
            model="  15" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.755 1.850
  nonbonded model="  15" pdb=" OD1 ASP A  74 "
            model="  15" pdb=" HG  SER A  76 "
     model   vdw
     1.770 1.850
  nonbonded model="  15" pdb=" HD1 TYR A  81 "
            model="  15" pdb=" HH  TYR A  91 "
     model   vdw
     1.811 2.100
  ... (remaining 28712 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.564)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.600 (Z=  1.343)
  Mean delta:    0.374 (Z=  0.204)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   89.659
  Mean delta:   24.317

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.094
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.045
    Angle     :  0.978   4.835   4077  Z= 0.341
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.764  89.659    768
    Min Nonbonded Distance : 1.570
  
  Molprobity Statistics.
    All-atom Clashscore : 20.30
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  : 15.33 %
      Favored  : 76.64 %
    Rotamer:
      Outliers : 27.42 %
      Allowed  : 16.94 %
      Favored  : 55.65 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.33 (0.47), residues: 137
    helix: -4.33 (0.28), residues: 60
    sheet:  None (None), residues: 0
    loop : -4.27 (0.57), residues: 77
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 135 
   PHE   0.001   0.001   PHE A  67 
   TYR   0.003   0.001   TYR A 111 
   ARG   0.001   0.000   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 135 
   PHE   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   TYR A 111 
   ARG   0.000   0.000   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  72  ASN

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   0" pdb=" CB  ILE A  51 "
        model="   0" pdb=" CB  LYS A  79 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1105
        1.03 -     1.23: 54
        1.23 -     1.43: 419
        1.43 -     1.62: 659
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" N   TYR A  89 "
       model="   0" pdb=" CA  TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.556 -0.098 1.90e-02 2.77e+03 2.67e+01
  bond model="   0" pdb=" N   LYS A  79 "
       model="   0" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.552 -0.094 1.90e-02 2.77e+03 2.43e+01
  bond model="   0" pdb=" CA  ASP A  88 "
       model="   0" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.612 -0.087 2.10e-02 2.27e+03 1.71e+01
  bond model="   0" pdb=" CA  ILE A  78 "
       model="   0" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.609 -0.084 2.10e-02 2.27e+03 1.61e+01
  bond model="   0" pdb=" C   PRO A 114 "
       model="   0" pdb=" N   ALA A 115 "
    ideal  model  delta    sigma   weight residual
    1.329  1.275  0.054 1.40e-02 5.10e+03 1.52e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       50.90 -    70.76: 1
       70.76 -    90.62: 1
       90.62 -   110.48: 2237
      110.48 -   130.34: 1832
      130.34 -   150.20: 6
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" N   TYR A  89 "
        model="   0" pdb=" CA  TYR A  89 "
        model="   0" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.00   50.90   59.10 3.00e+00 1.11e-01 3.88e+02
  angle model="   0" pdb=" C   ILE A  78 "
        model="   0" pdb=" N   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  150.20  -28.50 1.80e+00 3.09e-01 2.51e+02
  angle model="   0" pdb=" CB  TYR A  89 "
        model="   0" pdb=" CA  TYR A  89 "
        model="   0" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00  148.27  -39.27 3.00e+00 1.11e-01 1.71e+02
  angle model="   0" pdb=" N   TYR A  89 "
        model="   0" pdb=" CA  TYR A  89 "
        model="   0" pdb=" C   TYR A  89 "
      ideal   model   delta    sigma   weight residual
     111.00  134.44  -23.44 2.80e+00 1.28e-01 7.01e+01
  angle model="   0" pdb=" O   TYR A  89 "
        model="   0" pdb=" C   TYR A  89 "
        model="   0" pdb=" N   SER A  90 "
      ideal   model   delta    sigma   weight residual
     123.00  110.19   12.81 1.60e+00 3.91e-01 6.41e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.89: 975
       25.89 -    51.78: 38
       51.78 -    77.68: 10
       77.68 -   103.57: 3
      103.57 -   129.46: 2
  Dihedral angle restraints: 1028
    sinusoidal: 561
      harmonic: 467
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   50.54  129.46     0      5.00e+00 4.00e-02 6.70e+02
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   67.23  112.77     0      5.00e+00 4.00e-02 5.09e+02
  dihedral model="   0" pdb=" N   TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" CB  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  170.43  -47.63     0      2.50e+00 1.60e-01 3.63e+02
  ... (remaining 1025 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.188: 170
       1.188 -    2.375: 1
       2.375 -    3.562: 0
       3.562 -    4.748: 1
       4.748 -    5.935: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  79 "
            model="   0" pdb=" N   LYS A  79 "
            model="   0" pdb=" C   LYS A  79 "
            model="   0" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.42    5.94 2.00e-01 2.50e+01 8.81e+02
  chirality model="   0" pdb=" CB  ILE A  78 "
            model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" CG1 ILE A  78 "
            model="   0" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.59    5.23 2.00e-01 2.50e+01 6.84e+02
  chirality model="   0" pdb=" CB  THR A  92 "
            model="   0" pdb=" CA  THR A  92 "
            model="   0" pdb=" OG1 THR A  92 "
            model="   0" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.61    5.16 2.00e-01 2.50e+01 6.66e+02
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.359 2.00e-02 2.50e+03   1.63e-01 7.99e+02
        model="   0" pdb=" CG  TYR A  91 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.066 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.077 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.082 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.303 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.139 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.173 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.134 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.095 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.140 2.00e-02 2.50e+03   5.70e-02 9.76e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.102 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.102 2.00e-02 2.50e+03   4.68e-02 6.56e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.095 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.047 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 99
        2.13 -     2.75: 3929
        2.75 -     3.37: 6428
        3.37 -     3.98: 7635
        3.98 -     4.60: 11780
  Nonbonded interactions: 29871
  Sorted by model distance:
  nonbonded model="   0" pdb=" H   TYR A  89 "
            model="   0" pdb=" HA  TYR A  89 "
     model   vdw
     1.513 1.816
  nonbonded model="   0" pdb=" HD3 LYS A  79 "
            model="   0" pdb=" H   TYR A  81 "
     model   vdw
     1.614 2.270
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.738 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.770 1.850
  nonbonded model="   0" pdb=" H   LEU A  93 "
            model="   0" pdb=" HB2 SER A  97 "
     model   vdw
     1.786 2.270
  ... (remaining 29866 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   8.03 %
                favored =  76.64 %
  Rotamer outliers      =  27.42 %
  C-beta deviations     =     0
  Clashscore            =  20.30
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.67

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.13
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 462
        1.42 -     1.61: 669
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="  10" pdb=" N   MET A   1 "
       model="  10" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.44e+00
  bond model="  10" pdb=" CD  ARG A 127 "
       model="  10" pdb=" NE  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.461 -0.003 1.40e-02 5.10e+03 6.03e-02
  bond model="  10" pdb=" CZ  ARG A  58 "
       model="  10" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.71e-02
  bond model="  10" pdb=" CZ  ARG A  58 "
       model="  10" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.70e-02
  bond model="  10" pdb=" NE  ARG A  58 "
       model="  10" pdb=" CZ  ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.326  1.328 -0.002 1.10e-02 8.26e+03 4.92e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.92 -   106.91: 68
      106.91 -   112.90: 2717
      112.90 -   118.89: 426
      118.89 -   124.88: 824
      124.88 -   130.87: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="  10" pdb=" CB  PRO A 102 "
        model="  10" pdb=" CA  PRO A 102 "
        model="  10" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="  10" pdb=" CB  PRO A  22 "
        model="  10" pdb=" CA  PRO A  22 "
        model="  10" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="  10" pdb=" CB  PRO A 117 "
        model="  10" pdb=" CA  PRO A 117 "
        model="  10" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="  10" pdb=" CB  PRO A   6 "
        model="  10" pdb=" CA  PRO A   6 "
        model="  10" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="  10" pdb=" CB  PRO A  52 "
        model="  10" pdb=" CA  PRO A  52 "
        model="  10" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 879
       17.88 -    35.77: 79
       35.77 -    53.65: 52
       53.65 -    71.53: 19
       71.53 -    89.41: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="  10" pdb=" CB  GLU A  49 "
           model="  10" pdb=" CG  GLU A  49 "
           model="  10" pdb=" CD  GLU A  49 "
           model="  10" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.41  -89.41     1      3.00e+01 1.11e-03 1.06e+01
  dihedral model="  10" pdb=" N   LEU A   3 "
           model="  10" pdb=" CA  LEU A   3 "
           model="  10" pdb=" CB  LEU A   3 "
           model="  10" pdb=" CG  LEU A   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.18  -59.82     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="  10" pdb=" CA  MET A 128 "
           model="  10" pdb=" CB  MET A 128 "
           model="  10" pdb=" CG  MET A 128 "
           model="  10" pdb=" SD  MET A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.43  -59.43     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.019: 104
       0.019 -    0.038: 50
       0.038 -    0.056: 3
       0.056 -    0.075: 0
       0.075 -    0.093: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CA  ILE A 108 "
            model="  10" pdb=" N   ILE A 108 "
            model="  10" pdb=" C   ILE A 108 "
            model="  10" pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.17e-01
  chirality model="  10" pdb=" CA  ILE A 122 "
            model="  10" pdb=" N   ILE A 122 "
            model="  10" pdb=" C   ILE A 122 "
            model="  10" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.12e-01
  chirality model="  10" pdb=" CA  ILE A  51 "
            model="  10" pdb=" N   ILE A  51 "
            model="  10" pdb=" C   ILE A  51 "
            model="  10" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.12e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  PHE A  15 "    0.001 2.00e-02 2.50e+03   1.18e-03 4.18e-02
        model="  10" pdb=" CG  PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 PHE A  15 "    0.002 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 PHE A  15 "    0.002 2.00e-02 2.50e+03
        model="  10" pdb=" HZ  PHE A  15 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  81 "   -0.001 2.00e-02 2.50e+03   1.08e-03 3.48e-02
        model="  10" pdb=" CG  TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  81 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  PHE A  67 "   -0.001 2.00e-02 2.50e+03   1.02e-03 3.13e-02
        model="  10" pdb=" CG  PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 PHE A  67 "   -0.000 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 PHE A  67 "    0.002 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 PHE A  67 "   -0.002 2.00e-02 2.50e+03
        model="  10" pdb=" HZ  PHE A  67 "    0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 441
        2.29 -     2.87: 5264
        2.87 -     3.44: 5530
        3.44 -     4.02: 7200
        4.02 -     4.60: 10572
  Nonbonded interactions: 29007
  Sorted by model distance:
  nonbonded model="  10" pdb="HG23 ILE A  37 "
            model="  10" pdb="HG21 ILE A 108 "
     model   vdw
     1.710 2.440
  nonbonded model="  10" pdb="HG23 VAL A  41 "
            model="  10" pdb=" H   HIS A  43 "
     model   vdw
     1.711 2.270
  nonbonded model="  10" pdb=" O   GLU A  16 "
            model="  10" pdb=" HG1 THR A  20 "
     model   vdw
     1.771 1.850
  nonbonded model="  10" pdb="HD12 ILE A  37 "
            model="  10" pdb="HD22 LEU A  61 "
     model   vdw
     1.779 2.440
  nonbonded model="  10" pdb=" HD2 PRO A  22 "
            model="  10" pdb="HD12 LEU A  25 "
     model   vdw
     1.785 2.440
  ... (remaining 29002 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 125  LYS  CA
   A 125  LYS  C           1.52     1.42     0.11  2.10e-02  2.66e+01   5.2*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.40    -0.07  1.40e-02  2.55e+01   5.0*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.61    -0.09  2.10e-02  1.80e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.108 (Z=  5.154)
  Mean delta:    0.016 (Z=  0.831)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   135.99   -25.59  1.70e+00  2.27e+02  15.1*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   139.70   -28.30  1.90e+00  2.22e+02  14.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   100.02    16.18  2.00e+00  6.54e+01   8.1*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   132.50   -21.50  2.80e+00  5.90e+01   7.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.75   -13.05  1.80e+00  5.26e+01   7.2*sigma
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        121.70   134.69   -12.99  1.80e+00  5.21e+01   7.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.61   -10.71  1.50e+00  5.10e+01   7.1*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   122.23   -11.83  1.70e+00  4.84e+01   7.0*sigma
   A  86  ILE  N
   A  86  ILE  CA
   A  86  ILE  CB        111.50   122.96   -11.46  1.70e+00  4.54e+01   6.7*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    92.17    18.83  2.80e+00  4.52e+01   6.7*sigma
   A  82  THR  N
   A  82  THR  CA
   A  82  THR  CB        111.50   122.92   -11.42  1.70e+00  4.51e+01   6.7*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   122.49   -12.39  1.90e+00  4.25e+01   6.5*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.77   -11.07  1.80e+00  3.78e+01   6.1*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   119.52    -5.72  1.00e+00  3.27e+01   5.7*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.23    -5.63  1.00e+00  3.17e+01   5.6*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   131.77   -10.07  1.80e+00  3.13e+01   5.6*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.52   -10.92  2.00e+00  2.98e+01   5.5*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   131.46    -9.76  1.80e+00  2.94e+01   5.4*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  C         111.00    96.62    14.38  2.80e+00  2.64e+01   5.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   101.82     8.68  1.70e+00  2.61e+01   5.1*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  C         111.00   124.93   -13.93  2.80e+00  2.47e+01   5.0*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   130.55    -8.85  1.80e+00  2.42e+01   4.9*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30    99.55     9.75  2.00e+00  2.38e+01   4.9*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.42    -4.82  1.00e+00  2.33e+01   4.8*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   130.35    -8.65  1.80e+00  2.31e+01   4.8*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   125.62    -9.42  2.00e+00  2.22e+01   4.7*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00   124.14   -13.14  2.80e+00  2.20e+01   4.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O         120.80   112.96     7.84  1.70e+00  2.13e+01   4.6*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  C         111.00   123.81   -12.81  2.80e+00  2.09e+01   4.6*sigma
   A  86  ILE  CB
   A  86  ILE  CG1
   A  86  ILE  CD1       113.80   123.38    -9.58  2.10e+00  2.08e+01   4.6*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10   118.68    -8.58  1.90e+00  2.04e+01   4.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.49     5.71  1.30e+00  1.93e+01   4.4*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.24     4.36  1.00e+00  1.90e+01   4.4*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   117.75    -7.25  1.70e+00  1.82e+01   4.3*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   114.05     7.65  1.80e+00  1.81e+01   4.3*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    99.12    11.88  2.80e+00  1.80e+01   4.2*sigma
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG1       110.40   117.56    -7.16  1.70e+00  1.78e+01   4.2*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N         116.20   124.60    -8.40  2.00e+00  1.76e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.05    -5.65  1.40e+00  1.63e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:   28.305 (Z= 15.053)
  Mean delta:    2.974 (Z=  1.578)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   -94.41   -85.59  5.00e+00  2.93e+02  17.1*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00  -116.81   -63.19  5.00e+00  1.60e+02  12.6*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   119.79    60.21  5.00e+00  1.45e+02  12.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   120.88    59.12  5.00e+00  1.40e+02  11.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   121.18    58.82  5.00e+00  1.38e+02  11.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   123.72    56.28  5.00e+00  1.27e+02  11.3*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -133.98   -46.02  5.00e+00  8.47e+01   9.2*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   137.23    42.77  5.00e+00  7.32e+01   8.6*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   141.71    38.29  5.00e+00  5.87e+01   7.7*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   145.91    34.09  5.00e+00  4.65e+01   6.8*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   148.43    31.57  5.00e+00  3.99e+01   6.3*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   149.19    30.81  5.00e+00  3.80e+01   6.2*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -150.17   -29.83  5.00e+00  3.56e+01   6.0*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   150.27    29.73  5.00e+00  3.54e+01   5.9*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -156.02   -23.98  5.00e+00  2.30e+01   4.8*sigma
   A 111  TYR  CA
   A 111  TYR  C
   A 112  VAL  N
   A 112  VAL  CA        180.00   156.69    23.31  5.00e+00  2.17e+01   4.7*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00   157.22    22.78  5.00e+00  2.08e+01   4.6*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   158.17    21.83  5.00e+00  1.91e+01   4.4*sigma

  Min. delta:    0.035
  Max. delta:   89.573
  Mean delta:   17.626

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.36     5.87  2.00e-01  8.62e+02  29.4*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.39     5.03  2.00e-01  6.34e+02  25.2*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.23     4.74  2.00e-01  5.61e+02  23.7*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.14     4.65  2.00e-01  5.41e+02  23.3*sigma
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51    -1.99     4.50  2.00e-01  5.07e+02  22.5*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -1.76     4.20  2.00e-01  4.41e+02  21.0*sigma
   A  86  ILE  CB
   A  86  ILE  CA
   A  86  ILE  CG1
   A  86  ILE  CG2         2.64    -1.33     3.98  2.00e-01  3.95e+02  19.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.22     3.66  2.00e-01  3.34e+02  18.3*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -1.05     3.48  2.00e-01  3.03e+02  17.4*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43     1.01     1.43  2.00e-01  5.10e+01   7.1*sigma
   A 129  ARG  CA
   A 129  ARG  N
   A 129  ARG  C
   A 129  ARG  CB          2.51     1.17     1.34  2.00e-01  4.51e+01   6.7*sigma
   A  82  THR  CA
   A  82  THR  N
   A  82  THR  C
   A  82  THR  CB          2.53     1.57     0.96  2.00e-01  2.29e+01   4.8*sigma
   A 126  VAL  CB
   A 126  VAL  CA
   A 126  VAL  CG1
   A 126  VAL  CG2        -2.63    -1.71    -0.92  2.00e-01  2.13e+01   4.6*sigma

  Min. delta:    0.001
  Max. delta:    5.871
  Mean delta:    1.049

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.108       0.206      234.69  10.3*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O
   A  91  TYR  N             0.062       0.107       38.61   5.4*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.057       0.100       64.32   5.0*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O
   A 124  ALA  N             0.049       0.084       23.76   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.108
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  90  SER  HA , Angle N-CA-HA, observed: 123.056, delta from target: -13.056
   A  78  ILE  HB , Angle CA-CB-HB, observed: 94.599, delta from target: 14.401
   A  86  ILE  HA , Angle N-CA-HA, observed: 95.469, delta from target: 14.531
   A 126  VAL  HB , Angle CG2-CB-HB, observed: 93.302, delta from target: 14.698
   A  51  ILE  HA , Angle CB-CA-HA, observed: 93.755, delta from target: 15.245
   A  82  THR  HA , Angle N-CA-HA, observed: 93.873, delta from target: 16.127
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.697, delta from target: 16.303
   A 129  ARG  HA , Angle N-CA-HA, observed: 92.832, delta from target: 17.168
   A  78  ILE  HA , Angle C-CA-HA, observed: 91.151, delta from target: 17.849
   A  88  ASP  HA , Angle N-CA-HA, observed: 92.033, delta from target: 17.967
   A 129  ARG  HA , Angle C-CA-HA, observed: 90.720, delta from target: 18.280
   A  86  ILE  HB , Angle CG1-CB-HB, observed: 90.362, delta from target: 18.638
   A  77  ILE  HA , Angle C-CA-HA, observed: 90.347, delta from target: 18.653
   A  77  ILE  HA , Angle N-CA-HA, observed: 90.864, delta from target: 19.136
   A  78  ILE  HA , Angle CB-CA-HA, observed: 129.370, delta from target: -20.370
   A 126  VAL  HB , Angle CA-CB-HB, observed: 85.800, delta from target: 23.200
   A 126  VAL  HB , Angle CG1-CB-HB, observed: 131.481, delta from target: -23.481
   A 126  VAL  HA , Angle N-CA-HA, observed: 136.659, delta from target: -26.659
   A 126  VAL  HA , Angle CB-CA-HA, observed: 79.012, delta from target: 29.988
   A  78  ILE  HA , Angle N-CA-HA, observed: 75.740, delta from target: 34.260

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.108   2242  Z= 0.592
    Angle     :  2.791  34.260   4079  Z= 1.198
    Chirality :  1.049   5.871    176
    Planarity :  0.014   0.101    327
    Dihedral  : 14.886  89.573    769
    Min Nonbonded Distance : 1.399
  
  Molprobity Statistics.
    All-atom Clashscore : 16.68
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  9.49 %
      Favored  : 87.59 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  3.23 %
      Favored  : 89.52 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 9.16 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.16 (0.72), residues: 137
    helix: -1.77 (0.58), residues: 63
    sheet:  None (None), residues: 0
    loop : -2.43 (0.82), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.003   HIS A  43 
   PHE   0.072   0.012   PHE A  67 
   TYR   0.255   0.026   TYR A  50 
   ARG   0.021   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.003   HIS A  43 
   PHE   0.050   0.014   PHE A  67 
   TYR   0.206   0.031   TYR A  50 
   ARG   0.005   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.92 %
                favored =  87.59 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    16
  Clashscore            =  16.68
  RMS(bonds)            =   0.0115
  RMS(angles)           =   2.79
  MolProbity score      =   2.99

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.61    -0.15  1.90e-02  6.02e+01   7.8*sigma
   A 125  LYS  N
   A 125  LYS  CA          1.46     1.56    -0.10  1.90e-02  3.01e+01   5.5*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.55    -0.10  1.90e-02  2.60e+01   5.1*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.63    -0.10  2.10e-02  2.29e+01   4.8*sigma
   A 128  MET  CA
   A 128  MET  CB          1.53     1.62    -0.09  2.00e-02  1.86e+01   4.3*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.39    -0.06  1.40e-02  1.80e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.147 (Z=  7.758)
  Mean delta:    0.017 (Z=  0.900)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  CB        110.50    85.67    24.83  1.70e+00  2.13e+02  14.6*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10    87.16    22.94  1.90e+00  1.46e+02  12.1*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00   141.56   -30.56  2.80e+00  1.19e+02  10.9*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   128.14   -17.74  1.70e+00  1.09e+02  10.4*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   104.87    16.83  1.80e+00  8.74e+01   9.3*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40    94.74    16.66  1.90e+00  7.69e+01   8.8*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   106.08    15.62  1.80e+00  7.53e+01   8.7*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00   133.96   -22.96  2.80e+00  6.72e+01   8.2*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50    97.39    13.11  1.70e+00  5.95e+01   7.7*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   135.55   -13.85  1.80e+00  5.92e+01   7.7*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   134.99   -13.29  1.80e+00  5.45e+01   7.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.74   -13.04  1.80e+00  5.25e+01   7.2*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N         116.20   102.05    14.15  2.00e+00  5.00e+01   7.1*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   134.23   -12.53  1.80e+00  4.85e+01   7.0*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   134.22   -12.52  1.80e+00  4.84e+01   7.0*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 129  ARG  O         120.80   109.19    11.61  1.70e+00  4.66e+01   6.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O         120.80   109.24    11.56  1.70e+00  4.62e+01   6.8*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    97.76    12.34  1.90e+00  4.22e+01   6.5*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   133.07   -11.37  1.80e+00  3.99e+01   6.3*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.73   -11.03  1.80e+00  3.75e+01   6.1*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10   121.20   -11.10  1.90e+00  3.41e+01   5.8*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   132.08   -10.38  1.80e+00  3.33e+01   5.8*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   124.11     7.09  1.30e+00  2.97e+01   5.5*sigma
   A 106  ALA  N
   A 106  ALA  CA
   A 106  ALA  CB        110.40   102.28     8.12  1.50e+00  2.93e+01   5.4*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.42    -9.72  1.80e+00  2.92e+01   5.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.38   -10.78  2.00e+00  2.91e+01   5.4*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   120.21   -10.11  1.90e+00  2.83e+01   5.3*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80    99.11    11.69  2.20e+00  2.82e+01   5.3*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00   125.69   -14.69  2.80e+00  2.75e+01   5.2*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   117.82    -5.22  1.00e+00  2.73e+01   5.2*sigma
   A 123  GLU  CA
   A 123  GLU  CB
   A 123  GLU  CG        114.10   124.32   -10.22  2.00e+00  2.61e+01   5.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   126.39   -10.19  2.00e+00  2.60e+01   5.1*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   130.77    -9.07  1.80e+00  2.54e+01   5.0*sigma
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        121.70   130.76    -9.06  1.80e+00  2.53e+01   5.0*sigma
   A 122  ILE  C
   A 122  ILE  CA
   A 122  ILE  CB        111.60   101.65     9.95  2.00e+00  2.47e+01   5.0*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   119.48    -9.38  1.90e+00  2.44e+01   4.9*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   130.34    -8.64  1.80e+00  2.30e+01   4.8*sigma
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   117.38    -4.78  1.00e+00  2.28e+01   4.8*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   117.26    -4.66  1.00e+00  2.17e+01   4.7*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG2       110.50   118.39    -7.89  1.70e+00  2.16e+01   4.6*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   118.25    -7.75  1.70e+00  2.08e+01   4.6*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   123.76   -12.76  2.80e+00  2.08e+01   4.6*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   118.91    -9.81  2.20e+00  1.99e+01   4.5*sigma
   A 128  MET  CA
   A 128  MET  C
   A 128  MET  O         120.80   128.34    -7.54  1.70e+00  1.97e+01   4.4*sigma
   A 127  ARG  CA
   A 127  ARG  CB
   A 127  ARG  CG        114.10   105.34     8.76  2.00e+00  1.92e+01   4.4*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.27     4.33  1.00e+00  1.88e+01   4.3*sigma
   A  70  LEU  N
   A  70  LEU  CA
   A  70  LEU  CB        110.50   103.19     7.31  1.70e+00  1.85e+01   4.3*sigma
   A  52  PRO  C
   A  52  PRO  CA
   A  52  PRO  CB        110.10   118.15    -8.05  1.90e+00  1.80e+01   4.2*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  C         111.00   122.86   -11.86  2.80e+00  1.80e+01   4.2*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   129.32    -7.62  1.80e+00  1.79e+01   4.2*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   114.13     7.57  1.80e+00  1.77e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.76e+01   4.2*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   118.00    -4.20  1.00e+00  1.76e+01   4.2*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  ND1       122.70   128.99    -6.29  1.50e+00  1.76e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00    99.37    11.63  2.80e+00  1.72e+01   4.2*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   117.50    -7.00  1.70e+00  1.69e+01   4.1*sigma
   A  69  ALA  C
   A  70  LEU  N
   A  70  LEU  CA        121.70   129.10    -7.40  1.80e+00  1.69e+01   4.1*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.14    -5.74  1.40e+00  1.68e+01   4.1*sigma
   A 106  ALA  C
   A 106  ALA  CA
   A 106  ALA  CB        110.50   104.46     6.04  1.50e+00  1.62e+01   4.0*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   116.62    -4.02  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:   30.562 (Z= 14.604)
  Mean delta:    3.270 (Z=  1.730)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00    50.77   129.23  5.00e+00  6.68e+02  25.8*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00    71.40   108.60  5.00e+00  4.72e+02  21.7*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    96.73    83.27  5.00e+00  2.77e+02  16.7*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00  -103.01   -76.99  5.00e+00  2.37e+02  15.4*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   107.94    72.06  5.00e+00  2.08e+02  14.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -108.14   -71.86  5.00e+00  2.07e+02  14.4*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -110.58   -69.42  5.00e+00  1.93e+02  13.9*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   111.04    68.96  5.00e+00  1.90e+02  13.8*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   117.12    62.88  5.00e+00  1.58e+02  12.6*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -118.16   -61.84  5.00e+00  1.53e+02  12.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   119.72    60.28  5.00e+00  1.45e+02  12.1*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -121.45   -58.55  5.00e+00  1.37e+02  11.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   123.93    56.07  5.00e+00  1.26e+02  11.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   128.43    51.57  5.00e+00  1.06e+02  10.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -129.91   -50.09  5.00e+00  1.00e+02  10.0*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -135.72   -44.28  5.00e+00  7.84e+01   8.9*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   135.96    44.04  5.00e+00  7.76e+01   8.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   136.49    43.51  5.00e+00  7.57e+01   8.7*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -141.74   -38.26  5.00e+00  5.86e+01   7.7*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -147.92   -32.08  5.00e+00  4.12e+01   6.4*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -149.06   -30.94  5.00e+00  3.83e+01   6.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -149.38   -30.62  5.00e+00  3.75e+01   6.1*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA          0.00   -30.48    30.48  5.00e+00  3.72e+01   6.1*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00  -149.74   -30.26  5.00e+00  3.66e+01   6.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00  -150.33   -29.67  5.00e+00  3.52e+01   5.9*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -153.93   -26.07  5.00e+00  2.72e+01   5.2*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   156.91    23.09  5.00e+00  2.13e+01   4.6*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   159.45    20.55  5.00e+00  1.69e+01   4.1*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -159.67   -20.33  5.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.019
  Max. delta:  129.232
  Mean delta:   21.489

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -3.14     5.65  2.00e-01  7.99e+02  28.3*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.66     5.18  2.00e-01  6.71e+02  25.9*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.51     5.15  2.00e-01  6.64e+02  25.8*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  C
   A  52  PRO  CB          2.72    -2.30     5.02  2.00e-01  6.31e+02  25.1*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.36     4.91  2.00e-01  6.03e+02  24.6*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -2.30     4.78  2.00e-01  5.72e+02  23.9*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.06     4.57  2.00e-01  5.23e+02  22.9*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.86     4.37  2.00e-01  4.77e+02  21.9*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.86     4.30  2.00e-01  4.62e+02  21.5*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.71     4.14  2.00e-01  4.29e+02  20.7*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -1.36     3.87  2.00e-01  3.74e+02  19.3*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     0.37     2.15  2.00e-01  1.15e+02  10.7*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51     0.63     1.88  2.00e-01  8.79e+01   9.4*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43     3.27    -0.84  2.00e-01  1.75e+01   4.2*sigma

  Min. delta:    0.000
  Max. delta:    5.654
  Mean delta:    1.217

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 129  ARG  CA
   A 129  ARG  C
   A 129  ARG  O
   A 130  SER  N             0.110       0.190      121.24   9.5*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  93  LEU  O
   A  94  GLY  N             0.067       0.116       44.98   5.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O
   A 125  LYS  N             0.063       0.109       39.79   5.5*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O
   A 128  MET  N             0.061       0.106       37.48   5.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O
   A  93  LEU  N             0.051       0.089       26.43   4.4*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O
   A  80  GLY  N             0.051       0.088       26.13   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.149
  Mean delta:    0.022

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  89  TYR  HA , Angle N-CA-HA, observed: 98.000, delta from target: 12.000
   A  52  PRO  HA , Angle C-CA-HA, observed: 96.420, delta from target: 12.580
   A  89  TYR  HA , Angle C-CA-HA, observed: 96.231, delta from target: 12.769
   A 126  VAL  HA , Angle N-CA-HA, observed: 96.792, delta from target: 13.208
   A  51  ILE  HA , Angle CB-CA-HA, observed: 95.708, delta from target: 13.292
   A  77  ILE  HA , Angle C-CA-HA, observed: 95.572, delta from target: 13.428
   A  93  LEU  HA , Angle CB-CA-HA, observed: 122.505, delta from target: -13.505
   A  79  LYS  HA , Angle CB-CA-HA, observed: 94.641, delta from target: 14.359
   A 126  VAL  HB , Angle CG2-CB-HB, observed: 123.304, delta from target: -15.304
   A 126  VAL  HA , Angle CB-CA-HA, observed: 126.870, delta from target: -17.870
   A 126  VAL  HB , Angle CA-CB-HB, observed: 88.817, delta from target: 20.183
   A 125  LYS  HA , Angle C-CA-HA, observed: 80.196, delta from target: 28.804
   A 125  LYS  HA , Angle CB-CA-HA, observed: 142.454, delta from target: -33.454
   A 125  LYS  HA , Angle N-CA-HA, observed: 71.332, delta from target: 38.668
   A 128  MET  HA , Angle CB-CA-HA, observed: 150.135, delta from target: -41.135
   A  81  TYR  HA , Angle C-CA-HA, observed: 64.091, delta from target: 44.909

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.147   2242  Z= 0.641
    Angle     :  3.009  44.909   4079  Z= 1.299
    Chirality :  1.217   5.654    176
    Planarity :  0.016   0.115    327
    Dihedral  : 18.015 129.232    769
    Min Nonbonded Distance : 1.717
  
  Molprobity Statistics.
    All-atom Clashscore : 13.98
    Ramachandran Plot:
      Outliers : 14.60 %
      Allowed  : 10.22 %
      Favored  : 75.18 %
    Rotamer:
      Outliers : 10.48 %
      Allowed  :  4.03 %
      Favored  : 85.48 %
    Cbeta Deviations : 12.88 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 17.56 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.22 (0.63), residues: 137
    helix: -2.23 (0.53), residues: 70
    sheet:  None (None), residues: 0
    loop : -3.50 (0.70), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.081   0.015   PHE A  67 
   TYR   0.122   0.025   TYR A  91 
   ARG   0.125   0.014   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.041   0.013   PHE A  67 
   TYR   0.096   0.030   TYR A  91 
   ARG   0.005   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =  14.60 %
                favored =  75.18 %
  Rotamer outliers      =  10.48 %
  C-beta deviations     =    17
  Clashscore            =  13.98
  RMS(bonds)            =   0.0123
  RMS(angles)           =   3.01
  MolProbity score      =   3.22

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.063 (Z=  3.342)
  Mean delta:    0.014 (Z=  0.739)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   126.55   -14.95  2.00e+00  5.59e+01   7.5*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   123.41   -13.31  1.90e+00  4.91e+01   7.0*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.31   -12.61  1.80e+00  4.91e+01   7.0*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   133.78   -12.08  1.80e+00  4.51e+01   6.7*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   118.98    -6.38  1.00e+00  4.07e+01   6.4*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   120.61   -10.11  1.70e+00  3.54e+01   5.9*sigma
   A  70  LEU  N
   A  70  LEU  CA
   A  70  LEU  CB        110.50   100.61     9.89  1.70e+00  3.38e+01   5.8*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   125.39    -8.49  1.50e+00  3.20e+01   5.7*sigma
   A  86  ILE  C
   A  86  ILE  CA
   A  86  ILE  CB        111.60   122.67   -11.07  2.00e+00  3.06e+01   5.5*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   118.06    -5.46  1.00e+00  2.98e+01   5.5*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   131.20    -9.50  1.80e+00  2.79e+01   5.3*sigma
   A  15  PHE  CA
   A  15  PHE  CB
   A  15  PHE  CG        113.80   108.87     4.93  1.00e+00  2.43e+01   4.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.46    -4.86  1.00e+00  2.37e+01   4.9*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   106.66     9.54  2.00e+00  2.28e+01   4.8*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   120.99    -9.39  2.00e+00  2.21e+01   4.7*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   118.23    -7.73  1.70e+00  2.07e+01   4.5*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  C         111.00    98.79    12.21  2.80e+00  1.90e+01   4.4*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   118.14    -8.04  1.90e+00  1.79e+01   4.2*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   129.25    -7.55  1.80e+00  1.76e+01   4.2*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30   100.97     8.33  2.00e+00  1.74e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.70e+01   4.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    99.51    11.49  2.80e+00  1.68e+01   4.1*sigma
   A  69  ALA  C
   A  70  LEU  N
   A  70  LEU  CA        121.70   128.94    -7.24  1.80e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   14.947 (Z=  7.473)
  Mean delta:    2.333 (Z=  1.280)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -110.63   -69.37  5.00e+00  1.92e+02  13.9*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   127.13    52.87  5.00e+00  1.12e+02  10.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   134.90    45.10  5.00e+00  8.14e+01   9.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   141.24    38.76  5.00e+00  6.01e+01   7.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -144.36   -35.64  5.00e+00  5.08e+01   7.1*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00  -151.36   -28.64  5.00e+00  3.28e+01   5.7*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -155.15   -24.85  5.00e+00  2.47e+01   5.0*sigma
   A  70  LEU  CA
   A  70  LEU  C
   A  71  ILE  N
   A  71  ILE  CA        180.00   157.07    22.93  5.00e+00  2.10e+01   4.6*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -158.32   -21.68  5.00e+00  1.88e+01   4.3*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   158.48    21.52  5.00e+00  1.85e+01   4.3*sigma

  Min. delta:    0.057
  Max. delta:   84.273
  Mean delta:   14.720

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.14     5.65  2.00e-01  7.99e+02  28.3*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.52     5.17  2.00e-01  6.68e+02  25.8*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.40     4.91  2.00e-01  6.02e+02  24.5*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.02     4.45  2.00e-01  4.96e+02  22.3*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.61     4.12  2.00e-01  4.24e+02  20.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.11     3.54  2.00e-01  3.13e+02  17.7*sigma

  Min. delta:    0.000
  Max. delta:    5.655
  Mean delta:    0.879

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.095       0.169      179.09   8.5*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.074       0.132      108.16   6.6*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.065       0.123       83.30   6.2*sigma
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.079       0.091      109.93   4.5*sigma

  Min. delta:    0.000
  Max. delta:    0.095
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  78  ILE  HA , Angle C-CA-HA, observed: 96.949, delta from target: 12.051
   A  86  ILE  HA , Angle C-CA-HA, observed: 96.387, delta from target: 12.613
   A  81  TYR  HA , Angle CB-CA-HA, observed: 96.129, delta from target: 12.871
   A  89  TYR  HA , Angle C-CA-HA, observed: 91.039, delta from target: 17.961
   A  51  ILE  HA , Angle CB-CA-HA, observed: 89.131, delta from target: 19.869
   A  51  ILE  HA , Angle C-CA-HA, observed: 87.825, delta from target: 21.175

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.063   2242  Z= 0.526
    Angle     :  2.147  21.175   4079  Z= 0.950
    Chirality :  0.879   5.655    176
    Planarity :  0.013   0.088    327
    Dihedral  : 12.978  84.273    769
    Min Nonbonded Distance : 1.782
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.84 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  1.61 %
      Favored  : 93.55 %
    Cbeta Deviations :  7.58 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 3.82 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.60 (0.61), residues: 137
    helix: -1.86 (0.44), residues: 81
    sheet:  None (None), residues: 0
    loop : -1.25 (0.83), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A  43 
   PHE   0.190   0.026   PHE A  15 
   TYR   0.205   0.031   TYR A  50 
   ARG   0.026   0.006   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A  43 
   PHE   0.129   0.027   PHE A  15 
   TYR   0.169   0.035   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Ramachandran outliers =   2.19 %
                favored =  91.97 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =    10
  Clashscore            =   4.96
  RMS(bonds)            =   0.0101
  RMS(angles)           =   2.15
  MolProbity score      =   2.27

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.54    -0.09  1.60e-02  3.17e+01   5.6*sigma
   A  90  SER  N
   A  90  SER  CA          1.46     1.55    -0.10  1.90e-02  2.55e+01   5.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.096 (Z=  5.630)
  Mean delta:    0.015 (Z=  0.769)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   131.95   -21.85  1.90e+00  1.32e+02  11.5*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   120.65    -8.05  1.00e+00  6.48e+01   8.0*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   128.47   -14.37  2.00e+00  5.16e+01   7.2*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   109.54    12.16  1.80e+00  4.56e+01   6.8*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   133.46   -11.76  1.80e+00  4.27e+01   6.5*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  CB        111.50   100.72    10.78  1.70e+00  4.02e+01   6.3*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   110.33    11.37  1.80e+00  3.99e+01   6.3*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   121.12   -10.62  1.70e+00  3.90e+01   6.2*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG2       110.50   120.17    -9.67  1.70e+00  3.24e+01   5.7*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   127.30   -11.10  2.00e+00  3.08e+01   5.5*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.02    -5.42  1.00e+00  2.94e+01   5.4*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10    99.83    10.27  1.90e+00  2.92e+01   5.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   124.21     6.99  1.30e+00  2.89e+01   5.4*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   131.33    -9.63  1.80e+00  2.86e+01   5.4*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   117.76    -5.16  1.00e+00  2.67e+01   5.2*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   119.12    -8.62  1.70e+00  2.57e+01   5.1*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   104.92     7.08  1.40e+00  2.56e+01   5.1*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   130.27    -8.57  1.80e+00  2.26e+01   4.8*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.12    -4.52  1.00e+00  2.05e+01   4.5*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.44     5.76  1.30e+00  1.97e+01   4.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   120.29    -8.69  2.00e+00  1.89e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.76e+01   4.2*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  ND1       122.70   128.85    -6.15  1.50e+00  1.68e+01   4.1*sigma
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   128.96    -7.26  1.80e+00  1.63e+01   4.0*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  C         111.00   122.22   -11.22  2.80e+00  1.61e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:   21.845 (Z= 11.497)
  Mean delta:    2.520 (Z=  1.382)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -73.16  -106.84  5.00e+00  4.57e+02  21.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -100.06   -79.94  5.00e+00  2.56e+02  16.0*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   102.54    77.46  5.00e+00  2.40e+02  15.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -109.87   -70.13  5.00e+00  1.97e+02  14.0*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   125.26    54.74  5.00e+00  1.20e+02  10.9*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   129.47    50.53  5.00e+00  1.02e+02  10.1*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   138.17    41.83  5.00e+00  7.00e+01   8.4*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00  -138.22   -41.78  5.00e+00  6.98e+01   8.4*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   143.37    36.63  5.00e+00  5.37e+01   7.3*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   143.40    36.60  5.00e+00  5.36e+01   7.3*sigma
   A  70  LEU  CA
   A  70  LEU  C
   A  71  ILE  N
   A  71  ILE  CA        180.00   146.74    33.26  5.00e+00  4.43e+01   6.7*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   147.42    32.58  5.00e+00  4.25e+01   6.5*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   149.69    30.31  5.00e+00  3.67e+01   6.1*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   150.19    29.81  5.00e+00  3.56e+01   6.0*sigma
   A  50  TYR  CA
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        180.00   151.97    28.03  5.00e+00  3.14e+01   5.6*sigma
   A  71  ILE  CA
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        180.00  -152.68   -27.32  5.00e+00  2.98e+01   5.5*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   154.20    25.80  5.00e+00  2.66e+01   5.2*sigma
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00   157.77    22.23  5.00e+00  1.98e+01   4.4*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   158.68    21.32  5.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.003
  Max. delta:  106.841
  Mean delta:   19.603

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.24     4.75  2.00e-01  5.64e+02  23.7*sigma
   A 138  HIS  CA
   A 138  HIS  N
   A 138  HIS  C
   A 138  HIS  CB          2.51    -2.20     4.71  2.00e-01  5.54e+02  23.5*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.79     4.22  2.00e-01  4.45e+02  21.1*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51     1.15     1.36  2.00e-01  4.61e+01   6.8*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     1.41     1.10  2.00e-01  3.02e+01   5.5*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51     1.47     1.04  2.00e-01  2.68e+01   5.2*sigma

  Min. delta:    0.001
  Max. delta:    4.749
  Mean delta:    0.630

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.240       0.455     1151.37  22.8*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.071       0.125      100.61   6.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  76  SER  O
   A  77  ILE  N             0.051       0.089       26.25   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.240
  Mean delta:    0.024

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  81  TYR  HA , Angle N-CA-HA, observed: 97.619, delta from target: 12.381
   A  90  SER  HA , Angle N-CA-HA, observed: 94.038, delta from target: 15.962
   A  81  TYR  HA , Angle C-CA-HA, observed: 92.671, delta from target: 16.329
   A  74  ASP  HA , Angle N-CA-HA, observed: 126.407, delta from target: -16.407
   A  74  ASP  HA , Angle CB-CA-HA, observed: 90.570, delta from target: 18.430
   A  74  ASP  HA , Angle C-CA-HA, observed: 82.225, delta from target: 26.775

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.096   2242  Z= 0.547
    Angle     :  2.284  26.775   4079  Z= 1.017
    Chirality :  0.630   4.749    176
    Planarity :  0.020   0.273    327
    Dihedral  : 15.815 106.841    769
    Min Nonbonded Distance : 1.695
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  : 10.95 %
      Favored  : 83.21 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  8.87 %
      Favored  : 85.48 %
    Cbeta Deviations :  6.82 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 28.57 %
      Twisted General : 8.40 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.93 (0.62), residues: 137
    helix: -2.09 (0.50), residues: 72
    sheet:  None (None), residues: 0
    loop : -3.24 (0.73), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.040   0.014   PHE A  67 
   TYR   0.618   0.040   TYR A  91 
   ARG   0.030   0.004   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.032   0.013   PHE A  67 
   TYR   0.455   0.040   TYR A  91 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.691)
  Mean delta:    0.013 (Z=  0.668)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 130  SER  C
   A 130  SER  CA
   A 130  SER  CB        110.10    97.64    12.46  1.90e+00  4.30e+01   6.6*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   131.65    -9.95  1.80e+00  3.06e+01   5.5*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   124.45     6.75  1.30e+00  2.70e+01   5.2*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.90     4.70  1.00e+00  2.21e+01   4.7*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   117.92     6.48  1.40e+00  2.14e+01   4.6*sigma
   A  49  GLU  C
   A  49  GLU  CA
   A  49  GLU  CB        110.10   118.86    -8.76  1.90e+00  2.12e+01   4.6*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   117.20    -4.60  1.00e+00  2.12e+01   4.6*sigma
   A  49  GLU  N
   A  49  GLU  CA
   A  49  GLU  CB        110.50   102.87     7.63  1.70e+00  2.01e+01   4.5*sigma
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   121.78    -7.88  1.80e+00  1.92e+01   4.4*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.60     5.60  1.30e+00  1.86e+01   4.3*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   129.10    -7.40  1.80e+00  1.69e+01   4.1*sigma
   A  50  TYR  N
   A  50  TYR  CA
   A  50  TYR  CB        110.50   117.46    -6.96  1.70e+00  1.68e+01   4.1*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   119.17    -7.77  1.90e+00  1.67e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma
   A 129  ARG  C
   A 129  ARG  CA
   A 129  ARG  CB        110.10   117.79    -7.69  1.90e+00  1.64e+01   4.0*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N         116.20   124.22    -8.02  2.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   12.456 (Z=  6.556)
  Mean delta:    2.276 (Z=  1.228)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A   1  MET  CA
   A   1  MET  C
   A   2  LEU  N
   A   2  LEU  CA        180.00  -130.86   -49.14  5.00e+00  9.66e+01   9.8*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   138.04    41.96  5.00e+00  7.04e+01   8.4*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   153.19    26.81  5.00e+00  2.88e+01   5.4*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   155.24    24.76  5.00e+00  2.45e+01   5.0*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   156.24    23.76  5.00e+00  2.26e+01   4.8*sigma
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00   156.51    23.49  5.00e+00  2.21e+01   4.7*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00   159.11    20.89  5.00e+00  1.75e+01   4.2*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   159.95    20.05  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.004
  Max. delta:   69.423
  Mean delta:   17.513

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51    -2.16     4.67  2.00e-01  5.45e+02  23.3*sigma
   A   2  LEU  CA
   A   2  LEU  N
   A   2  LEU  C
   A   2  LEU  CB          2.51    -1.77     4.28  2.00e-01  4.59e+02  21.4*sigma

  Min. delta:    0.001
  Max. delta:    4.669
  Mean delta:    0.491

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.234       0.215     1091.38  10.8*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.186       0.195      690.29   9.7*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.142       0.147      400.56   7.3*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  ND1
   A 136  HIS  CD2
   A 136  HIS  CE1
   A 136  HIS  NE2           0.100       0.127      150.28   6.3*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.054       0.096       59.02   4.8*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.089       0.090      156.74   4.5*sigma
   A  68  TYR  CB
   A  68  TYR  CG
   A  68  TYR  CD1
   A  68  TYR  CD2
   A  68  TYR  CE1
   A  68  TYR  CE2
   A  68  TYR  CZ
   A  68  TYR  OH            0.044       0.088       39.36   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.234
  Mean delta:    0.030

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  50  TYR  HA , Angle N-CA-HA, observed: 97.856, delta from target: 12.144
   A   2  LEU  HA , Angle C-CA-HA, observed: 94.813, delta from target: 14.187

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.476
    Angle     :  2.021  14.187   4079  Z= 0.898
    Chirality :  0.491   4.669    176
    Planarity :  0.023   0.238    327
    Dihedral  : 15.053  74.866    769
    Min Nonbonded Distance : 1.749
  
  Molprobity Statistics.
    All-atom Clashscore : 13.07
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  : 10.22 %
      Favored  : 86.13 %
    Rotamer:
      Outliers : 10.48 %
      Allowed  :  7.26 %
      Favored  : 82.26 %
    Cbeta Deviations :  4.55 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 1.53 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.61 (0.70), residues: 137
    helix: -1.34 (0.55), residues: 70
    sheet:  None (None), residues: 0
    loop : -2.14 (0.84), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.027   0.009   HIS A  43 
   PHE   0.072   0.017   PHE A  15 
   TYR   0.515   0.074   TYR A 111 
   ARG   0.049   0.012   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.027   0.009   HIS A  43 
   PHE   0.047   0.015   PHE A  15 
   TYR   0.389   0.080   TYR A 111 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   5.84 %
                favored =  83.21 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     9
  Clashscore            =   7.66
  RMS(bonds)            =   0.0105
  RMS(angles)           =   2.28
  MolProbity score      =   2.68

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   3.65 %
                favored =  86.13 %
  Rotamer outliers      =  10.48 %
  C-beta deviations     =     6
  Clashscore            =  13.07
  RMS(bonds)            =   0.0092
  RMS(angles)           =   2.02
  MolProbity score      =   3.04

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.57    -0.12  1.60e-02  5.87e+01   7.7*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.123 (Z=  7.665)
  Mean delta:    0.014 (Z=  0.755)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   140.27   -29.27  2.80e+00  1.09e+02  10.5*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   106.69    15.01  1.80e+00  6.95e+01   8.3*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   127.99   -16.39  2.00e+00  6.71e+01   8.2*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   107.18    14.52  1.80e+00  6.51e+01   8.1*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   120.48    -7.88  1.00e+00  6.20e+01   7.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.93   -11.03  1.50e+00  5.41e+01   7.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   130.19   -13.99  2.00e+00  4.89e+01   7.0*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   132.82   -11.12  1.80e+00  3.82e+01   6.2*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   113.28     9.72  1.60e+00  3.69e+01   6.1*sigma
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   131.75   -10.05  1.80e+00  3.12e+01   5.6*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.16    -5.56  1.00e+00  3.10e+01   5.6*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.61    -9.91  1.80e+00  3.03e+01   5.5*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   119.83    -9.33  1.70e+00  3.01e+01   5.5*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   131.45    -9.75  1.80e+00  2.94e+01   5.4*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.34   -10.74  2.00e+00  2.89e+01   5.4*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   106.27     9.93  2.00e+00  2.47e+01   5.0*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   119.48    -9.38  1.90e+00  2.44e+01   4.9*sigma
   A  80  GLY  N
   A  80  GLY  CA
   A  80  GLY  C         113.30    99.72    13.58  2.90e+00  2.19e+01   4.7*sigma
   A  84  GLU  C
   A  84  GLU  CA
   A  84  GLU  CB        110.10   101.55     8.55  1.90e+00  2.02e+01   4.5*sigma
   A  95  ASP  C
   A  95  ASP  CA
   A  95  ASP  CB        110.10   118.60    -8.50  1.90e+00  2.00e+01   4.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.44     5.76  1.30e+00  1.96e+01   4.4*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   118.01    -7.51  1.70e+00  1.95e+01   4.4*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   121.76    -7.86  1.80e+00  1.91e+01   4.4*sigma
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        121.70   129.45    -7.75  1.80e+00  1.85e+01   4.3*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.37    -5.97  1.40e+00  1.82e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   116.77    -4.17  1.00e+00  1.74e+01   4.2*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG1       110.40   117.38    -6.98  1.70e+00  1.69e+01   4.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  97  SER  O         120.80   127.77    -6.97  1.70e+00  1.68e+01   4.1*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   122.28    -8.18  2.00e+00  1.67e+01   4.1*sigma
   A  43  HIS  CA
   A  43  HIS  CB
   A  43  HIS  CG        113.80   117.88    -4.08  1.00e+00  1.67e+01   4.1*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   114.40     7.30  1.80e+00  1.64e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.56     4.04  1.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   29.272 (Z= 10.454)
  Mean delta:    2.544 (Z=  1.362)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -59.79  -120.21  5.00e+00  5.78e+02  24.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -101.48   -78.52  5.00e+00  2.47e+02  15.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   112.59    67.41  5.00e+00  1.82e+02  13.5*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   115.75    64.25  5.00e+00  1.65e+02  12.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -117.53   -62.47  5.00e+00  1.56e+02  12.5*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   128.26    51.74  5.00e+00  1.07e+02  10.3*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00  -143.68   -36.32  5.00e+00  5.28e+01   7.3*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   146.46    33.54  5.00e+00  4.50e+01   6.7*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -150.19   -29.81  5.00e+00  3.56e+01   6.0*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   151.04    28.96  5.00e+00  3.35e+01   5.8*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -151.28   -28.72  5.00e+00  3.30e+01   5.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -152.65   -27.35  5.00e+00  2.99e+01   5.5*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   158.32    21.68  5.00e+00  1.88e+01   4.3*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -159.11   -20.89  5.00e+00  1.75e+01   4.2*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -159.94   -20.06  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.031
  Max. delta:  120.209
  Mean delta:   17.553

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.93     5.44  2.00e-01  7.40e+02  27.2*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.47     5.00  2.00e-01  6.25e+02  25.0*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.44     4.95  2.00e-01  6.14e+02  24.8*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.34     4.89  2.00e-01  5.99e+02  24.5*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.17     4.82  2.00e-01  5.80e+02  24.1*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.20     4.63  2.00e-01  5.37e+02  23.2*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.85     3.28  2.00e-01  2.69e+02  16.4*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     0.97     1.54  2.00e-01  5.92e+01   7.7*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43     1.58     0.85  2.00e-01  1.81e+01   4.3*sigma

  Min. delta:    0.000
  Max. delta:    5.441
  Mean delta:    0.968

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  84  GLU  CA
   A  84  GLU  C
   A  84  GLU  O
   A  85  LYS  N             0.054       0.093       28.72   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.069
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  77  ILE  HA , Angle CB-CA-HA, observed: 95.485, delta from target: 13.515
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.259, delta from target: 17.741
   A  77  ILE  HA , Angle C-CA-HA, observed: 89.811, delta from target: 19.189
   A  51  ILE  HA , Angle CB-CA-HA, observed: 89.550, delta from target: 19.450
   A  89  TYR  HA , Angle C-CA-HA, observed: 88.498, delta from target: 20.502
   A  89  TYR  HA , Angle CB-CA-HA, observed: 142.974, delta from target: -33.974
   A  89  TYR  HA , Angle N-CA-HA, observed: 73.231, delta from target: 36.769

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.123   2242  Z= 0.538
    Angle     :  2.385  36.769   4079  Z= 1.030
    Chirality :  0.968   5.441    176
    Planarity :  0.011   0.069    327
    Dihedral  : 14.476 120.209    769
    Min Nonbonded Distance : 1.491
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  7.30 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  1.61 %
      Favored  : 91.94 %
    Cbeta Deviations :  8.33 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 6.11 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.63 (0.57), residues: 137
    helix: -2.34 (0.42), residues: 80
    sheet:  None (None), residues: 0
    loop : -2.34 (0.76), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A  43 
   PHE   0.063   0.012   PHE A  67 
   TYR   0.131   0.018   TYR A  12 
   ARG   0.041   0.008   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A  43 
   PHE   0.046   0.014   PHE A  67 
   TYR   0.108   0.019   TYR A  12 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.68    -0.15  2.10e-02  5.20e+01   7.2*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.59    -0.13  1.90e-02  4.57e+01   6.8*sigma
   A 123  GLU  N
   A 123  GLU  CA          1.46     1.35     0.11  1.90e-02  3.15e+01   5.6*sigma
   A 123  GLU  C
   A 124  ALA  N           1.33     1.26     0.07  1.40e-02  2.75e+01   5.2*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.27     0.06  1.40e-02  1.71e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.151 (Z=  7.211)
  Mean delta:    0.017 (Z=  0.868)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   131.87   -21.37  1.70e+00  1.58e+02  12.6*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   139.72   -18.02  1.80e+00  1.00e+02  10.0*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   124.28   -13.78  1.50e+00  8.44e+01   9.2*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20    99.34    16.86  2.00e+00  7.10e+01   8.4*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   124.66   -14.16  1.70e+00  6.94e+01   8.3*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   136.43   -14.73  1.80e+00  6.70e+01   8.2*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40    98.44    11.96  1.50e+00  6.35e+01   8.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.95   -11.05  1.50e+00  5.43e+01   7.4*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   134.94   -13.24  1.80e+00  5.41e+01   7.4*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   134.31   -12.61  1.80e+00  4.91e+01   7.0*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   121.85   -11.35  1.70e+00  4.46e+01   6.7*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   124.71   -13.11  2.00e+00  4.30e+01   6.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   131.93   -11.13  1.70e+00  4.28e+01   6.5*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O         120.80   131.66   -10.86  1.70e+00  4.08e+01   6.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   103.58    12.62  2.00e+00  3.98e+01   6.3*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   124.21   -12.61  2.00e+00  3.98e+01   6.3*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   132.44   -10.74  1.80e+00  3.56e+01   6.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   127.84   -11.64  2.00e+00  3.39e+01   5.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   104.81    11.39  2.00e+00  3.24e+01   5.7*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.01    -5.41  1.00e+00  2.93e+01   5.4*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   114.72     8.28  1.60e+00  2.68e+01   5.2*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   112.74     8.96  1.80e+00  2.48e+01   5.0*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.39    -4.79  1.00e+00  2.29e+01   4.8*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   118.56    -8.06  1.70e+00  2.25e+01   4.7*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   117.90     4.70  1.00e+00  2.21e+01   4.7*sigma
   A 122  ILE  O
   A 122  ILE  C
   A 123  GLU  N         123.00   130.46    -7.46  1.60e+00  2.18e+01   4.7*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   130.07    -8.37  1.80e+00  2.16e+01   4.7*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   118.90    -8.80  1.90e+00  2.15e+01   4.6*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.29     5.91  1.30e+00  2.07e+01   4.5*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   102.87     7.63  1.70e+00  2.02e+01   4.5*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.47     5.73  1.30e+00  1.94e+01   4.4*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   129.60    -7.90  1.80e+00  1.92e+01   4.4*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80   101.19     9.61  2.20e+00  1.91e+01   4.4*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   129.31    -7.61  1.80e+00  1.79e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   121.47    -7.57  1.80e+00  1.77e+01   4.2*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   118.27    -9.17  2.20e+00  1.74e+01   4.2*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   129.20    -7.50  1.80e+00  1.73e+01   4.2*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   103.52     7.88  1.90e+00  1.72e+01   4.1*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  C         111.00   122.58   -11.58  2.80e+00  1.71e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.86     6.94  1.70e+00  1.67e+01   4.1*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   129.03    -7.33  1.80e+00  1.66e+01   4.1*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   128.99    -7.29  1.80e+00  1.64e+01   4.0*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG1       110.40   117.28    -6.88  1.70e+00  1.64e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   21.373 (Z= 12.572)
  Mean delta:    2.761 (Z=  1.525)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    50.24   129.76  5.00e+00  6.74e+02  26.0*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    62.05   117.95  5.00e+00  5.57e+02  23.6*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    67.73   112.27  5.00e+00  5.04e+02  22.5*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00    92.12    87.88  5.00e+00  3.09e+02  17.6*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    94.12    85.88  5.00e+00  2.95e+02  17.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   122.27    57.73  5.00e+00  1.33e+02  11.5*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   127.78    52.22  5.00e+00  1.09e+02  10.4*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   128.91    51.09  5.00e+00  1.04e+02  10.2*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   131.16    48.84  5.00e+00  9.54e+01   9.8*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -132.83   -47.17  5.00e+00  8.90e+01   9.4*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -134.77   -45.23  5.00e+00  8.18e+01   9.0*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   140.41    39.59  5.00e+00  6.27e+01   7.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   143.94    36.06  5.00e+00  5.20e+01   7.2*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA          0.00    32.01   -32.01  5.00e+00  4.10e+01   6.4*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   150.92    29.08  5.00e+00  3.38e+01   5.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   154.15    25.85  5.00e+00  2.67e+01   5.2*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -155.02   -24.98  5.00e+00  2.50e+01   5.0*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -156.73   -23.27  5.00e+00  2.17e+01   4.7*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   157.06    22.94  5.00e+00  2.10e+01   4.6*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   157.14    22.86  5.00e+00  2.09e+01   4.6*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -157.86   -22.14  5.00e+00  1.96e+01   4.4*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -159.89   -20.11  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.002
  Max. delta:  129.762
  Mean delta:   19.614

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.46     4.97  2.00e-01  6.19e+02  24.9*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.44     4.95  2.00e-01  6.13e+02  24.8*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.41     4.92  2.00e-01  6.06e+02  24.6*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.09     4.60  2.00e-01  5.28e+02  23.0*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.10     3.53  2.00e-01  3.12e+02  17.7*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43     1.61     0.83  2.00e-01  1.71e+01   4.1*sigma

  Min. delta:    0.002
  Max. delta:    4.975
  Mean delta:    0.799

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O
   A 124  ALA  N             0.073       0.126       53.59   6.3*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.059       0.112       69.96   5.6*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.062       0.109       77.38   5.5*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.051       0.088       51.21   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.073
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 122  ILE  HA , Angle CB-CA-HA, observed: 96.522, delta from target: 12.478
   A  92  THR  HB , Angle CA-CB-HB, observed: 96.404, delta from target: 12.596
   A  77  ILE  HA , Angle C-CA-HA, observed: 95.577, delta from target: 13.423
   A 127  ARG  HA , Angle N-CA-HA, observed: 96.528, delta from target: 13.472
   A 129  ARG  HA , Angle N-CA-HA, observed: 95.205, delta from target: 14.795
   A 124  ALA  HA , Angle C-CA-HA, observed: 93.705, delta from target: 15.295
   A  77  ILE  HA , Angle CB-CA-HA, observed: 93.635, delta from target: 15.365
   A  78  ILE  HB , Angle CA-CB-HB, observed: 93.226, delta from target: 15.774
   A 127  ARG  HA , Angle CB-CA-HA, observed: 92.821, delta from target: 16.179
   A  51  ILE  HA , Angle CB-CA-HA, observed: 91.677, delta from target: 17.323
   A 127  ARG  HA , Angle C-CA-HA, observed: 126.928, delta from target: -17.928
   A  51  ILE  HA , Angle C-CA-HA, observed: 89.454, delta from target: 19.546

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.151   2242  Z= 0.618
    Angle     :  2.427  21.373   4079  Z= 1.101
    Chirality :  0.799   4.975    176
    Planarity :  0.013   0.077    327
    Dihedral  : 16.125 129.762    769
    Min Nonbonded Distance : 1.345
  
  Molprobity Statistics.
    All-atom Clashscore : 21.64
    Ramachandran Plot:
      Outliers :  8.76 %
      Allowed  :  8.03 %
      Favored  : 83.21 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  5.65 %
      Favored  : 87.90 %
    Cbeta Deviations :  9.85 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 10.69 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.43 (0.68), residues: 137
    helix: -1.23 (0.57), residues: 60
    sheet:  None (None), residues: 0
    loop : -1.96 (0.74), residues: 77
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.004   HIS A  43 
   PHE   0.039   0.013   PHE A  15 
   TYR   0.141   0.029   TYR A  50 
   ARG   0.057   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.004   HIS A  43 
   PHE   0.028   0.014   PHE A  15 
   TYR   0.112   0.031   TYR A  50 
   ARG   0.001   0.000   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.037 (Z=  2.802)
  Mean delta:    0.012 (Z=  0.642)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        121.70   130.90    -9.20  1.80e+00  2.61e+01   5.1*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   124.76     6.44  1.30e+00  2.45e+01   5.0*sigma
   A 137  HIS  CA
   A 137  HIS  CB
   A 137  HIS  CG        113.80   109.00     4.80  1.00e+00  2.30e+01   4.8*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.82     4.78  1.00e+00  2.29e+01   4.8*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   118.13    -4.33  1.00e+00  1.88e+01   4.3*sigma
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG1       110.40   117.50    -7.10  1.70e+00  1.74e+01   4.2*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    9.202 (Z=  5.112)
  Mean delta:    1.957 (Z=  1.088)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   158.13    21.87  5.00e+00  1.91e+01   4.4*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   159.87    20.13  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.014
  Max. delta:   88.828
  Mean delta:   19.243

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.392
  Mean delta:    0.106

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.089       0.156      158.97   7.8*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.080       0.155      127.04   7.8*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  ND1
   A 137  HIS  CD2
   A 137  HIS  CE1
   A 137  HIS  NE2           0.087       0.153      113.57   7.7*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.106       0.148      224.52   7.4*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.064       0.124       82.88   6.2*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  ND1
   A 135  HIS  CD2
   A 135  HIS  CE1
   A 135  HIS  NE2           0.088       0.116      116.43   5.8*sigma

  Min. delta:    0.000
  Max. delta:    0.158
  Mean delta:    0.024

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.457
    Angle     :  1.790   9.202   4079  Z= 0.802
    Chirality :  0.106   0.392    176
    Planarity :  0.019   0.140    327
    Dihedral  : 16.239  88.828    769
    Min Nonbonded Distance : 1.727
  
  Molprobity Statistics.
    All-atom Clashscore : 12.17
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  8.03 %
      Favored  : 90.51 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  8.87 %
      Favored  : 85.48 %
    Cbeta Deviations :  1.52 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.67 (0.59), residues: 137
    helix: -0.01 (0.55), residues: 62
    sheet:  None (None), residues: 0
    loop : -2.15 (0.59), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.040   0.013   HIS A 137 
   PHE   0.117   0.024   PHE A  45 
   TYR   0.235   0.045   TYR A  89 
   ARG   0.134   0.021   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.040   0.013   HIS A 137 
   PHE   0.060   0.019   PHE A  45 
   TYR   0.156   0.045   TYR A  81 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   4.38 %
                favored =  88.32 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    11
  Clashscore            =   6.76
  RMS(bonds)            =   0.0102
  RMS(angles)           =   2.38
  MolProbity score      =   2.58

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   8.76 %
                favored =  83.21 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    13
  Clashscore            =  21.64
  RMS(bonds)            =   0.0119
  RMS(angles)           =   2.43
  MolProbity score      =   3.13

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  90.51 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     2
  Clashscore            =  12.17
  RMS(bonds)            =   0.0088
  RMS(angles)           =   1.79
  MolProbity score      =   2.70

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.53    -0.08  1.60e-02  2.48e+01   5.0*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.62    -0.09  2.10e-02  1.86e+01   4.3*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.38     0.08  1.90e-02  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.090 (Z=  4.982)
  Mean delta:    0.016 (Z=  0.844)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   129.30   -18.80  1.50e+00  1.57e+02  12.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.49   -11.59  1.50e+00  5.97e+01   7.7*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   109.44    12.26  1.80e+00  4.64e+01   6.8*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   129.47   -13.27  2.00e+00  4.40e+01   6.6*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   121.59   -11.09  1.70e+00  4.26e+01   6.5*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   122.45   -12.35  1.90e+00  4.23e+01   6.5*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.39   -10.69  1.80e+00  3.53e+01   5.9*sigma
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        121.70   132.38   -10.68  1.80e+00  3.52e+01   5.9*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.32   -10.62  1.80e+00  3.48e+01   5.9*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   121.19   -11.09  1.90e+00  3.41e+01   5.8*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   132.05   -10.35  1.80e+00  3.31e+01   5.7*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   124.14   -12.84  2.30e+00  3.12e+01   5.6*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   131.36    -9.66  1.80e+00  2.88e+01   5.4*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N         116.20   105.57    10.63  2.00e+00  2.83e+01   5.3*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   126.78   -10.58  2.00e+00  2.80e+01   5.3*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.11   -10.51  2.00e+00  2.76e+01   5.3*sigma
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   131.10    -9.40  1.80e+00  2.73e+01   5.2*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    96.39    14.61  2.80e+00  2.72e+01   5.2*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  CB        110.50   101.93     8.57  1.70e+00  2.54e+01   5.0*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   115.09     7.91  1.60e+00  2.44e+01   4.9*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  C         111.00   124.71   -13.71  2.80e+00  2.40e+01   4.9*sigma
   A 123  GLU  CA
   A 123  GLU  CB
   A 123  GLU  CG        114.10   123.85    -9.75  2.00e+00  2.37e+01   4.9*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   123.83    -9.73  2.00e+00  2.37e+01   4.9*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   130.39    -8.69  1.80e+00  2.33e+01   4.8*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   130.29    -8.59  1.80e+00  2.28e+01   4.8*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  C         111.00   124.15   -13.15  2.80e+00  2.21e+01   4.7*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   129.96    -8.26  1.80e+00  2.10e+01   4.6*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG1       110.40   118.16    -7.76  1.70e+00  2.08e+01   4.6*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  C         111.00    98.33    12.67  2.80e+00  2.05e+01   4.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.34     5.86  1.30e+00  2.03e+01   4.5*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N         116.20   107.40     8.80  2.00e+00  1.94e+01   4.4*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   116.85    -4.25  1.00e+00  1.81e+01   4.3*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   129.29    -7.59  1.80e+00  1.78e+01   4.2*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   102.11     7.99  1.90e+00  1.77e+01   4.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.73     7.07  1.70e+00  1.73e+01   4.2*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  C         111.00   122.59   -11.59  2.80e+00  1.71e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG2       110.50   117.40    -6.90  1.70e+00  1.65e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.54     4.06  1.00e+00  1.65e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   18.797 (Z= 12.532)
  Mean delta:    2.802 (Z=  1.500)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    70.64   109.36  5.00e+00  4.78e+02  21.9*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   103.45    76.55  5.00e+00  2.34e+02  15.3*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -105.34   -74.66  5.00e+00  2.23e+02  14.9*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   106.05    73.95  5.00e+00  2.19e+02  14.8*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   114.75    65.25  5.00e+00  1.70e+02  13.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   116.72    63.28  5.00e+00  1.60e+02  12.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -120.26   -59.74  5.00e+00  1.43e+02  11.9*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   121.62    58.38  5.00e+00  1.36e+02  11.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   135.34    44.66  5.00e+00  7.98e+01   8.9*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA          0.00   -41.33    41.33  5.00e+00  6.83e+01   8.3*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -139.61   -40.39  5.00e+00  6.52e+01   8.1*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00  -141.01   -38.99  5.00e+00  6.08e+01   7.8*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00  -143.78   -36.22  5.00e+00  5.25e+01   7.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -146.06   -33.94  5.00e+00  4.61e+01   6.8*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   150.99    29.01  5.00e+00  3.37e+01   5.8*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   157.69    22.31  5.00e+00  1.99e+01   4.5*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   157.97    22.03  5.00e+00  1.94e+01   4.4*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -158.52   -21.48  5.00e+00  1.85e+01   4.3*sigma

  Min. delta:    0.020
  Max. delta:  109.365
  Mean delta:   18.239

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.39     5.90  2.00e-01  8.69e+02  29.5*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.93     5.44  2.00e-01  7.40e+02  27.2*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.67     5.32  2.00e-01  7.06e+02  26.6*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.76     5.27  2.00e-01  6.93e+02  26.3*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.54     5.19  2.00e-01  6.73e+02  25.9*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.20     4.84  2.00e-01  5.87e+02  24.2*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51    -2.30     4.81  2.00e-01  5.78e+02  24.1*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.33     4.76  2.00e-01  5.66e+02  23.8*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.84     3.27  2.00e-01  2.68e+02  16.4*sigma

  Min. delta:    0.000
  Max. delta:    5.896
  Mean delta:    1.150

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.121       0.111      292.06   5.5*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.044       0.085       38.33   4.3*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.046       0.081       42.21   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.121
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    3" pdbres="HIS A  43  conformer  : HE2, HD1 
    3" pdbres="HIS A 134  conformer  : HE2, HD1 
    3" pdbres="HIS A 135  conformer  : HE2, HD1 
    3" pdbres="HIS A 136  conformer  : HE2, HD1 
    3" pdbres="HIS A 137  conformer  : HE2, HD1 
    3" pdbres="HIS A 138  conformer  : HE2, HD1 
    3" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  97  SER  HA , Angle CB-CA-HA, observed: 121.175, delta from target: -12.175
   A  83  THR  HA , Angle N-CA-HA, observed: 97.414, delta from target: 12.586
   A 124  ALA  HA , Angle N-CA-HA, observed: 122.861, delta from target: -12.861
   A  89  TYR  HA , Angle C-CA-HA, observed: 95.911, delta from target: 13.089
   A  97  SER  HA , Angle N-CA-HA, observed: 96.210, delta from target: 13.790
   A  74  ASP  HA , Angle C-CA-HA, observed: 94.920, delta from target: 14.080
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.543, delta from target: 17.457
   A  51  ILE  HA , Angle CB-CA-HA, observed: 89.666, delta from target: 19.334
   A 124  ALA  HA , Angle CB-CA-HA, observed: 86.606, delta from target: 22.394

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.090   2242  Z= 0.601
    Angle     :  2.458  22.394   4079  Z= 1.091
    Chirality :  1.150   5.896    176
    Planarity :  0.012   0.113    327
    Dihedral  : 14.764 109.365    769
    Min Nonbonded Distance : 1.627
  
  Molprobity Statistics.
    All-atom Clashscore : 14.88
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  : 13.14 %
      Favored  : 80.29 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  6.45 %
      Favored  : 89.52 %
    Cbeta Deviations :  9.09 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 10.69 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.57 (0.64), residues: 137
    helix: -1.66 (0.54), residues: 64
    sheet:  None (None), residues: 0
    loop : -3.14 (0.70), residues: 73
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A 135 
   PHE   0.042   0.011   PHE A  45 
   TYR   0.288   0.025   TYR A  89 
   ARG   0.051   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A 135 
   PHE   0.030   0.009   PHE A  45 
   TYR   0.231   0.030   TYR A  89 
   ARG   0.010   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Ramachandran outliers =   6.57 %
                favored =  80.29 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =    12
  Clashscore            =  14.88
  RMS(bonds)            =   0.0115
  RMS(angles)           =   2.46
  MolProbity score      =   2.87

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.59    -0.13  1.90e-02  4.70e+01   6.9*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.56    -0.11  1.60e-02  4.61e+01   6.8*sigma
   A  92  THR  CA
   A  92  THR  C           1.52     1.42     0.11  2.10e-02  2.73e+01   5.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.130 (Z=  6.855)
  Mean delta:    0.017 (Z=  0.873)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   141.85   -20.15  1.80e+00  1.25e+02  11.2*sigma
   A  93  LEU  CD1
   A  93  LEU  CG
   A  93  LEU  CD2       110.80   127.54   -16.74  2.20e+00  5.79e+01   7.6*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   135.11   -13.41  1.80e+00  5.55e+01   7.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.72   -10.82  1.50e+00  5.20e+01   7.2*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   122.50   -12.00  1.70e+00  4.98e+01   7.1*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   134.18   -12.48  1.80e+00  4.81e+01   6.9*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   102.70    13.50  2.00e+00  4.55e+01   6.7*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   124.58   -12.98  2.00e+00  4.21e+01   6.5*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.91   -11.21  1.80e+00  3.88e+01   6.2*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40    99.84    11.56  1.90e+00  3.70e+01   6.1*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   132.44   -10.74  1.80e+00  3.56e+01   6.0*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   120.38    -9.88  1.70e+00  3.38e+01   5.8*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  C         111.00   126.98   -15.98  2.80e+00  3.26e+01   5.7*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.23    -5.63  1.00e+00  3.16e+01   5.6*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   119.70    -9.30  1.70e+00  2.99e+01   5.5*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.41    -9.71  1.80e+00  2.91e+01   5.4*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   119.37    -8.87  1.70e+00  2.72e+01   5.2*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   119.02    -8.52  1.70e+00  2.51e+01   5.0*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   106.27     9.93  2.00e+00  2.46e+01   5.0*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   106.31     9.89  2.00e+00  2.45e+01   4.9*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   118.90    -8.40  1.70e+00  2.44e+01   4.9*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   130.57    -8.87  1.80e+00  2.43e+01   4.9*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.53    -4.93  1.00e+00  2.43e+01   4.9*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   130.42    -8.72  1.80e+00  2.35e+01   4.8*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   118.69    -8.19  1.70e+00  2.32e+01   4.8*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   103.42     8.08  1.70e+00  2.26e+01   4.8*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   130.25    -8.55  1.80e+00  2.26e+01   4.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   120.81    -9.21  2.00e+00  2.12e+01   4.6*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.24     5.96  1.30e+00  2.10e+01   4.6*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   103.88     7.62  1.70e+00  2.01e+01   4.5*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O         120.80   128.31    -7.51  1.70e+00  1.95e+01   4.4*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   128.17    -7.37  1.70e+00  1.88e+01   4.3*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10   101.93     8.17  1.90e+00  1.85e+01   4.3*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.31     4.29  1.00e+00  1.84e+01   4.3*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.67     5.53  1.30e+00  1.81e+01   4.3*sigma
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   129.36    -7.66  1.80e+00  1.81e+01   4.3*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N         116.20   107.72     8.48  2.00e+00  1.80e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.70e+01   4.1*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.09    -5.69  1.40e+00  1.65e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   20.148 (Z= 11.194)
  Mean delta:    2.848 (Z=  1.525)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -55.06  -124.94  5.00e+00  6.24e+02  25.0*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    58.46   121.54  5.00e+00  5.91e+02  24.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00    66.51   113.49  5.00e+00  5.15e+02  22.7*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   109.60    70.40  5.00e+00  1.98e+02  14.1*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -110.54   -69.46  5.00e+00  1.93e+02  13.9*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   116.08    63.92  5.00e+00  1.63e+02  12.8*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00  -116.38   -63.62  5.00e+00  1.62e+02  12.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   116.76    63.24  5.00e+00  1.60e+02  12.6*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   121.02    58.98  5.00e+00  1.39e+02  11.8*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   121.07    58.93  5.00e+00  1.39e+02  11.8*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -128.60   -51.40  5.00e+00  1.06e+02  10.3*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -128.75   -51.25  5.00e+00  1.05e+02  10.2*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   135.69    44.31  5.00e+00  7.85e+01   8.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   141.71    38.29  5.00e+00  5.86e+01   7.7*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   142.33    37.67  5.00e+00  5.68e+01   7.5*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   144.16    35.84  5.00e+00  5.14e+01   7.2*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   145.20    34.80  5.00e+00  4.85e+01   7.0*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   145.51    34.49  5.00e+00  4.76e+01   6.9*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   147.15    32.85  5.00e+00  4.32e+01   6.6*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   154.92    25.08  5.00e+00  2.52e+01   5.0*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -155.19   -24.81  5.00e+00  2.46e+01   5.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -156.96   -23.04  5.00e+00  2.12e+01   4.6*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -157.02   -22.98  5.00e+00  2.11e+01   4.6*sigma

  Min. delta:    0.037
  Max. delta:  124.936
  Mean delta:   19.990

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -3.15     5.66  2.00e-01  8.00e+02  28.3*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.11     5.62  2.00e-01  7.90e+02  28.1*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -2.82     5.33  2.00e-01  7.11e+02  26.7*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.54     5.18  2.00e-01  6.71e+02  25.9*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.42     5.06  2.00e-01  6.40e+02  25.3*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.42     4.97  2.00e-01  6.18e+02  24.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.94     4.38  2.00e-01  4.79e+02  21.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.90     3.33  2.00e-01  2.78e+02  16.7*sigma
   A  93  LEU  CG
   A  93  LEU  CB
   A  93  LEU  CD1
   A  93  LEU  CD2        -2.59    -1.19    -1.40  2.00e-01  4.87e+01   7.0*sigma

  Min. delta:    0.001
  Max. delta:    5.659
  Mean delta:    1.083

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.055       0.108       60.87   5.4*sigma

  Min. delta:    0.000
  Max. delta:    0.062
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    3" pdbres="HIS A  43  conformer  : HE2, HD1 
    3" pdbres="HIS A 134  conformer  : HE2, HD1 
    3" pdbres="HIS A 135  conformer  : HE2, HD1 
    3" pdbres="HIS A 136  conformer  : HE2, HD1 
    3" pdbres="HIS A 137  conformer  : HE2, HD1 
    3" pdbres="HIS A 138  conformer  : HE2, HD1 
    3" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  93  LEU  HA , Angle N-CA-HA, observed: 97.854, delta from target: 12.146
   A  78  ILE  HB , Angle CA-CB-HB, observed: 96.554, delta from target: 12.446
   A  92  THR  HA , Angle C-CA-HA, observed: 96.268, delta from target: 12.732
   A 126  VAL  HB , Angle CA-CB-HB, observed: 95.744, delta from target: 13.256
   A  90  SER  HA , Angle N-CA-HA, observed: 96.662, delta from target: 13.338
   A 131  ILE  HA , Angle C-CA-HA, observed: 95.606, delta from target: 13.394
   A  51  ILE  HA , Angle CB-CA-HA, observed: 94.415, delta from target: 14.585
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.716, delta from target: 17.284
   A  98  SER  HA , Angle N-CA-HA, observed: 92.358, delta from target: 17.642
   A  93  LEU  HG , Angle CD2-CG-HG, observed: 80.383, delta from target: 27.617

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.130   2242  Z= 0.622
    Angle     :  2.508  27.617   4079  Z= 1.112
    Chirality :  1.083   5.659    176
    Planarity :  0.011   0.061    327
    Dihedral  : 16.586 124.936    769
    Min Nonbonded Distance : 1.158
  
  Molprobity Statistics.
    All-atom Clashscore : 15.78
    Ramachandran Plot:
      Outliers : 11.68 %
      Allowed  : 11.68 %
      Favored  : 76.64 %
    Rotamer:
      Outliers :  8.06 %
      Allowed  :  4.03 %
      Favored  : 87.90 %
    Cbeta Deviations : 11.36 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 14.50 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.42 (0.72), residues: 137
    helix: -1.69 (0.59), residues: 63
    sheet:  None (None), residues: 0
    loop : -2.89 (0.80), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.003   HIS A 139 
   PHE   0.064   0.020   PHE A  15 
   TYR   0.159   0.021   TYR A  91 
   ARG   0.021   0.006   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.003   HIS A 139 
   PHE   0.027   0.016   PHE A  67 
   TYR   0.121   0.024   TYR A  91 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =  11.68 %
                favored =  76.64 %
  Rotamer outliers      =   8.06 %
  C-beta deviations     =    15
  Clashscore            =  15.78
  RMS(bonds)            =   0.0119
  RMS(angles)           =   2.51
  MolProbity score      =   3.17

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 127  ARG  CA
   A 127  ARG  CB          1.53     1.63    -0.10  2.00e-02  2.41e+01   4.9*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.098 (Z=  4.913)
  Mean delta:    0.015 (Z=  0.806)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   123.11   -10.51  1.00e+00  1.10e+02  10.5*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   131.46   -14.56  1.50e+00  9.42e+01   9.7*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   125.93   -15.43  1.70e+00  8.24e+01   9.1*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   125.19   -15.09  1.90e+00  6.31e+01   7.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.73   -11.83  1.50e+00  6.22e+01   7.9*sigma
   A 116  ASP  O
   A 116  ASP  C
   A 117  PRO  N         123.00   111.02    11.98  1.60e+00  5.60e+01   7.5*sigma
   A 116  ASP  N
   A 116  ASP  CA
   A 116  ASP  CB        110.50    97.93    12.57  1.70e+00  5.47e+01   7.4*sigma
   A 129  ARG  CA
   A 129  ARG  CB
   A 129  ARG  CG        114.10   128.00   -13.90  2.00e+00  4.83e+01   6.9*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   133.55   -11.85  1.80e+00  4.34e+01   6.6*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  CB        110.50    99.92    10.58  1.70e+00  3.87e+01   6.2*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   110.84    10.86  1.80e+00  3.64e+01   6.0*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   119.94    -9.84  1.90e+00  2.68e+01   5.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   117.48     5.12  1.00e+00  2.62e+01   5.1*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   112.24     8.56  1.70e+00  2.53e+01   5.0*sigma
   A 127  ARG  CA
   A 127  ARG  CB
   A 127  ARG  CG        114.10   124.13   -10.03  2.00e+00  2.52e+01   5.0*sigma
   A 116  ASP  C
   A 116  ASP  CA
   A 116  ASP  CB        110.10   118.89    -8.79  1.90e+00  2.14e+01   4.6*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N         116.20   124.94    -8.74  2.00e+00  1.91e+01   4.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.39     7.41  1.70e+00  1.90e+01   4.4*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.70     5.50  1.30e+00  1.79e+01   4.2*sigma
   A 100  GLN  CG
   A 100  GLN  CD
   A 100  GLN  NE2       116.40   122.68    -6.28  1.50e+00  1.76e+01   4.2*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  C         111.00    99.50    11.50  2.80e+00  1.69e+01   4.1*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   106.38     5.62  1.40e+00  1.61e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   15.434 (Z= 10.507)
  Mean delta:    2.482 (Z=  1.368)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   -65.36  -114.64  5.00e+00  5.26e+02  22.9*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00  -128.14   -51.86  5.00e+00  1.08e+02  10.4*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00  -144.64   -35.36  5.00e+00  5.00e+01   7.1*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   145.17    34.83  5.00e+00  4.85e+01   7.0*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00  -149.96   -30.04  5.00e+00  3.61e+01   6.0*sigma
   A  52  PRO  CA
   A  52  PRO  C
   A  53  LEU  N
   A  53  LEU  CA        180.00  -155.49   -24.51  5.00e+00  2.40e+01   4.9*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   156.43    23.57  5.00e+00  2.22e+01   4.7*sigma

  Min. delta:    0.002
  Max. delta:  114.635
  Mean delta:   20.695

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.12     1.39  2.00e-01  4.81e+01   6.9*sigma

  Min. delta:    0.000
  Max. delta:    1.387
  Mean delta:    0.148

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.053       0.099       55.93   4.9*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.042       0.081       35.36   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.199
  Mean delta:    0.027

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 128  MET  HA , Angle N-CA-HA, observed: 123.069, delta from target: -13.069
   A 128  MET  HA , Angle C-CA-HA, observed: 96.360, delta from target: 13.640
   A 127  ARG  HA , Angle C-CA-HA, observed: 93.888, delta from target: 15.112
   A 129  ARG  HA , Angle C-CA-HA, observed: 125.255, delta from target: -16.255

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.098   2242  Z= 0.574
    Angle     :  2.138  16.255   4079  Z= 0.978
    Chirality :  0.148   1.387    176
    Planarity :  0.019   0.157    327
    Dihedral  : 16.725 114.635    769
    Min Nonbonded Distance : 1.618
  
  Molprobity Statistics.
    All-atom Clashscore : 16.68
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  5.84 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  9.68 %
      Allowed  : 12.10 %
      Favored  : 78.23 %
    Cbeta Deviations :  3.03 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 3.82 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.52 (0.57), residues: 137
    helix: -1.41 (0.53), residues: 69
    sheet:  None (None), residues: 0
    loop : -3.44 (0.57), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A 139 
   PHE   0.132   0.035   PHE A  15 
   TYR   0.167   0.030   TYR A  50 
   ARG   0.172   0.030   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A 139 
   PHE   0.063   0.025   PHE A  15 
   TYR   0.130   0.032   TYR A  12 
   ARG   0.015   0.003   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.032 (Z=  1.547)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.619 (Z=  1.352)
  Mean delta:    0.375 (Z=  0.206)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   89.320
  Mean delta:   23.643

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.094
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.032   2241  Z= 0.045
    Angle     :  0.980   4.862   4077  Z= 0.342
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.002    326
    Dihedral  : 18.822  89.320    768
    Min Nonbonded Distance : 1.547
  
  Molprobity Statistics.
    All-atom Clashscore : 18.49
    Ramachandran Plot:
      Outliers :  5.11 %
      Allowed  : 14.60 %
      Favored  : 80.29 %
    Rotamer:
      Outliers : 22.58 %
      Allowed  : 15.32 %
      Favored  : 62.10 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.36 (0.50), residues: 137
    helix: -4.12 (0.36), residues: 54
    sheet:  None (None), residues: 0
    loop : -4.56 (0.55), residues: 83
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 134 
   PHE   0.002   0.001   PHE A  15 
   TYR   0.003   0.001   TYR A  12 
   ARG   0.001   0.000   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 134 
   PHE   0.001   0.000   PHE A  67 
   TYR   0.001   0.000   TYR A  12 
   ARG   0.000   0.000   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 134  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.56    -0.11  1.60e-02  4.90e+01   7.0*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.61    -0.09  2.10e-02  1.81e+01   4.3*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.44     0.09  2.10e-02  1.75e+01   4.2*sigma
   A  88  ASP  C
   A  89  TYR  N           1.33     1.39    -0.06  1.40e-02  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.112 (Z=  7.003)
  Mean delta:    0.016 (Z=  0.833)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   127.58   -17.08  1.70e+00  1.01e+02  10.0*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   131.09   -19.79  2.30e+00  7.40e+01   8.6*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   136.95   -15.25  1.80e+00  7.18e+01   8.5*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   130.44   -16.34  2.00e+00  6.67e+01   8.2*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   128.32   -14.42  1.80e+00  6.42e+01   8.0*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   135.18   -13.48  1.80e+00  5.61e+01   7.5*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   123.55   -13.45  1.90e+00  5.01e+01   7.1*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50    99.06    11.44  1.70e+00  4.53e+01   6.7*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   118.96    -6.36  1.00e+00  4.05e+01   6.4*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   111.04    10.66  1.80e+00  3.51e+01   5.9*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   100.48    10.02  1.70e+00  3.48e+01   5.9*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   132.08   -10.38  1.80e+00  3.33e+01   5.8*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.36    -5.76  1.00e+00  3.32e+01   5.8*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   113.82     9.18  1.60e+00  3.29e+01   5.7*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   126.90   -15.90  2.80e+00  3.23e+01   5.7*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   120.55   -10.45  1.90e+00  3.02e+01   5.5*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.26    -9.56  1.80e+00  2.82e+01   5.3*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   131.27    -8.27  1.60e+00  2.67e+01   5.2*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   119.15    -8.75  1.70e+00  2.65e+01   5.1*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   119.05    -8.55  1.70e+00  2.53e+01   5.0*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   124.81   -13.81  2.80e+00  2.43e+01   4.9*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   122.69    -8.79  1.80e+00  2.39e+01   4.9*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   130.49    -8.79  1.80e+00  2.38e+01   4.9*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   117.48    -4.88  1.00e+00  2.38e+01   4.9*sigma
   A  51  ILE  N
   A  51  ILE  CA
   A  51  ILE  C         111.00   123.62   -12.62  2.80e+00  2.03e+01   4.5*sigma
   A  99  LEU  N
   A  99  LEU  CA
   A  99  LEU  C         111.00   123.50   -12.50  2.80e+00  1.99e+01   4.5*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   129.67    -7.97  1.80e+00  1.96e+01   4.4*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   118.48    -8.38  1.90e+00  1.95e+01   4.4*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   129.56    -7.86  1.80e+00  1.91e+01   4.4*sigma
   A 101  LYS  CA
   A 101  LYS  CB
   A 101  LYS  CG        114.10   122.77    -8.67  2.00e+00  1.88e+01   4.3*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    99.28    11.72  2.80e+00  1.75e+01   4.2*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   129.20    -7.50  1.80e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG2       110.50   117.42    -6.92  1.70e+00  1.66e+01   4.1*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.93     5.27  1.30e+00  1.64e+01   4.1*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.94     5.26  1.30e+00  1.64e+01   4.0*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.58     4.02  1.00e+00  1.61e+01   4.0*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   116.61    -4.01  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   19.790 (Z= 10.049)
  Mean delta:    2.810 (Z=  1.494)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00    62.17   117.83  5.00e+00  5.55e+02  23.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   -74.36  -105.64  5.00e+00  4.46e+02  21.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00    84.18    95.82  5.00e+00  3.67e+02  19.2*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   100.00    80.00  5.00e+00  2.56e+02  16.0*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   126.39    53.61  5.00e+00  1.15e+02  10.7*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   129.15    50.85  5.00e+00  1.03e+02  10.2*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   129.45    50.55  5.00e+00  1.02e+02  10.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -129.52   -50.48  5.00e+00  1.02e+02  10.1*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   132.90    47.10  5.00e+00  8.87e+01   9.4*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   138.06    41.94  5.00e+00  7.04e+01   8.4*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA          0.00    40.48   -40.48  5.00e+00  6.56e+01   8.1*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   143.50    36.50  5.00e+00  5.33e+01   7.3*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   144.55    35.45  5.00e+00  5.03e+01   7.1*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   146.75    33.25  5.00e+00  4.42e+01   6.7*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   147.77    32.23  5.00e+00  4.16e+01   6.4*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   148.19    31.81  5.00e+00  4.05e+01   6.4*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   150.12    29.88  5.00e+00  3.57e+01   6.0*sigma
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00   150.74    29.26  5.00e+00  3.42e+01   5.9*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   151.48    28.52  5.00e+00  3.25e+01   5.7*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -152.45   -27.55  5.00e+00  3.04e+01   5.5*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -152.80   -27.20  5.00e+00  2.96e+01   5.4*sigma
   A   3  LEU  CA
   A   3  LEU  C
   A   4  ILE  N
   A   4  ILE  CA        180.00   153.51    26.49  5.00e+00  2.81e+01   5.3*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   153.68    26.32  5.00e+00  2.77e+01   5.3*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA          0.00   -26.07    26.07  5.00e+00  2.72e+01   5.2*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -155.08   -24.92  5.00e+00  2.48e+01   5.0*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -156.28   -23.72  5.00e+00  2.25e+01   4.7*sigma

  Min. delta:    0.003
  Max. delta:  117.831
  Mean delta:   19.585

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.37     5.88  2.00e-01  8.64e+02  29.4*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.93     5.57  2.00e-01  7.76e+02  27.8*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -2.46     4.97  2.00e-01  6.17e+02  24.8*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.24     4.76  2.00e-01  5.67e+02  23.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.57     4.01  2.00e-01  4.01e+02  20.0*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.19     3.62  2.00e-01  3.28e+02  18.1*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -0.28     2.79  2.00e-01  1.95e+02  14.0*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51     1.02     1.49  2.00e-01  5.54e+01   7.4*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     1.43     1.08  2.00e-01  2.91e+01   5.4*sigma

  Min. delta:    0.002
  Max. delta:    5.879
  Mean delta:    0.947

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O
   A 127  ARG  N             0.054       0.093       28.93   4.6*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O
   A  80  GLY  N             0.049       0.085       24.33   4.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  89  TYR  O
   A  90  SER  N             0.049       0.085       24.22   4.3*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.048       0.084       46.87   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.149
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  89  TYR  HA , Angle N-CA-HA, observed: 97.506, delta from target: 12.494
   A 130  SER  HA , Angle N-CA-HA, observed: 96.956, delta from target: 13.044
   A  97  SER  HA , Angle C-CA-HA, observed: 95.771, delta from target: 13.229
   A  99  LEU  HA , Angle N-CA-HA, observed: 96.608, delta from target: 13.392
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.075, delta from target: 15.925
   A  93  LEU  HG , Angle CB-CG-HG, observed: 93.063, delta from target: 15.937
   A  97  SER  HA , Angle CB-CA-HA, observed: 92.841, delta from target: 16.159
   A  91  TYR  HA , Angle N-CA-HA, observed: 93.099, delta from target: 16.901
   A  90  SER  HA , Angle N-CA-HA, observed: 92.615, delta from target: 17.385
   A  51  ILE  HA , Angle N-CA-HA, observed: 90.995, delta from target: 19.005
   A  89  TYR  HA , Angle CB-CA-HA, observed: 136.503, delta from target: -27.503
   A  90  SER  HA , Angle CB-CA-HA, observed: 81.000, delta from target: 28.000
   A  89  TYR  HA , Angle C-CA-HA, observed: 45.499, delta from target: 63.501

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.112   2242  Z= 0.593
    Angle     :  2.719  63.501   4079  Z= 1.154
    Chirality :  0.947   5.879    176
    Planarity :  0.015   0.149    327
    Dihedral  : 16.373 117.831    769
    Min Nonbonded Distance : 1.462
  
  Molprobity Statistics.
    All-atom Clashscore : 14.88
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  : 10.22 %
      Favored  : 81.75 %
    Rotamer:
      Outliers :  9.68 %
      Allowed  :  3.23 %
      Favored  : 87.10 %
    Cbeta Deviations :  9.85 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 1.53 %
      Twisted Proline : 14.29 %
      Twisted General : 11.45 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.74 (0.56), residues: 137
    helix: -2.91 (0.42), residues: 76
    sheet:  None (None), residues: 0
    loop : -3.41 (0.71), residues: 61
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A 136 
   PHE   0.087   0.016   PHE A  67 
   TYR   0.112   0.022   TYR A  12 
   ARG   0.050   0.009   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A 136 
   PHE   0.059   0.016   PHE A  67 
   TYR   0.093   0.024   TYR A  12 
   ARG   0.004   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   4.38 %
                favored =  89.78 %
  Rotamer outliers      =   9.68 %
  C-beta deviations     =     4
  Clashscore            =  16.68
  RMS(bonds)            =   0.0110
  RMS(angles)           =   2.14
  MolProbity score      =   3.03

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.55    -0.09  1.90e-02  2.50e+01   5.0*sigma
   A  79  LYS  CA
   A  79  LYS  CB          1.53     1.62    -0.09  2.00e-02  2.14e+01   4.6*sigma
   A  77  ILE  N
   A  77  ILE  CA          1.46     1.55    -0.09  1.90e-02  2.10e+01   4.6*sigma
   A  93  LEU  N
   A  93  LEU  CA          1.46     1.38     0.08  1.90e-02  1.81e+01   4.3*sigma
   A  92  THR  CA
   A  92  THR  C           1.52     1.44     0.09  2.10e-02  1.77e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.004)
  Max. delta:    0.105 (Z=  4.999)
  Mean delta:    0.016 (Z=  0.831)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    84.54    25.56  1.90e+00  1.81e+02  13.5*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50    95.50    15.00  1.70e+00  7.78e+01   8.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20    98.61    17.59  2.00e+00  7.73e+01   8.8*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   130.37   -19.07  2.30e+00  6.88e+01   8.3*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   125.05   -14.95  1.90e+00  6.19e+01   7.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.26   -11.36  1.50e+00  5.74e+01   7.6*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   134.26   -12.56  1.80e+00  4.87e+01   7.0*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   134.00   -12.30  1.80e+00  4.67e+01   6.8*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.70   -11.00  1.80e+00  3.73e+01   6.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   120.60   -10.10  1.70e+00  3.53e+01   5.9*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   124.44   -10.54  1.80e+00  3.43e+01   5.9*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   121.05   -10.95  1.90e+00  3.32e+01   5.8*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    99.35    10.75  1.90e+00  3.20e+01   5.7*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.23    -5.63  1.00e+00  3.17e+01   5.6*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   112.04     9.66  1.80e+00  2.88e+01   5.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   130.81    -9.11  1.80e+00  2.56e+01   5.1*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   119.59    -9.49  1.90e+00  2.50e+01   5.0*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   124.84     6.36  1.30e+00  2.40e+01   4.9*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   102.08     9.52  2.00e+00  2.27e+01   4.8*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   130.08    -8.38  1.80e+00  2.17e+01   4.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O         120.80   128.62    -7.82  1.70e+00  2.12e+01   4.6*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.19    -4.59  1.00e+00  2.11e+01   4.6*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   120.67    -9.07  2.00e+00  2.05e+01   4.5*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   118.08    -7.68  1.70e+00  2.04e+01   4.5*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   122.93    -8.83  2.00e+00  1.95e+01   4.4*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.57    -6.17  1.40e+00  1.94e+01   4.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   107.60     8.60  2.00e+00  1.85e+01   4.3*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   117.69    -7.29  1.70e+00  1.84e+01   4.3*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.72     5.48  1.30e+00  1.78e+01   4.2*sigma
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        121.70   114.17     7.53  1.80e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   117.53    -7.03  1.70e+00  1.71e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.88     6.92  1.70e+00  1.66e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   25.564 (Z= 13.455)
  Mean delta:    2.640 (Z=  1.437)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00    69.64   110.36  5.00e+00  4.87e+02  22.1*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   -75.37  -104.63  5.00e+00  4.38e+02  20.9*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   -82.34   -97.66  5.00e+00  3.81e+02  19.5*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -114.00   -66.00  5.00e+00  1.74e+02  13.2*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -123.64   -56.36  5.00e+00  1.27e+02  11.3*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -124.99   -55.01  5.00e+00  1.21e+02  11.0*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   126.76    53.24  5.00e+00  1.13e+02  10.6*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -127.45   -52.55  5.00e+00  1.10e+02  10.5*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00   137.53    42.47  5.00e+00  7.22e+01   8.5*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   138.34    41.66  5.00e+00  6.94e+01   8.3*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -138.92   -41.08  5.00e+00  6.75e+01   8.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -145.56   -34.44  5.00e+00  4.75e+01   6.9*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00  -149.02   -30.98  5.00e+00  3.84e+01   6.2*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   152.41    27.59  5.00e+00  3.05e+01   5.5*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -154.95   -25.05  5.00e+00  2.51e+01   5.0*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   156.20    23.80  5.00e+00  2.27e+01   4.8*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   156.64    23.36  5.00e+00  2.18e+01   4.7*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -158.59   -21.41  5.00e+00  1.83e+01   4.3*sigma

  Min. delta:    0.001
  Max. delta:  110.358
  Mean delta:   17.827

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.08     5.59  2.00e-01  7.80e+02  27.9*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.43     5.07  2.00e-01  6.43e+02  25.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.39     4.94  2.00e-01  6.10e+02  24.7*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.05     4.70  2.00e-01  5.52e+02  23.5*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.16     4.68  2.00e-01  5.49e+02  23.4*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.10     4.54  2.00e-01  5.15e+02  22.7*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.24     3.75  2.00e-01  3.52e+02  18.8*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.10     3.53  2.00e-01  3.12e+02  17.7*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43     3.24    -0.81  2.00e-01  1.63e+01   4.0*sigma

  Min. delta:    0.002
  Max. delta:    5.586
  Mean delta:    1.000

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.141       0.244      399.82  12.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O
   A  80  GLY  N             0.073       0.126       53.37   6.3*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O
   A  91  TYR  N             0.061       0.105       36.93   5.3*sigma

  Min. delta:    0.000
  Max. delta:    0.141
  Mean delta:    0.021

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  51  ILE  HA , Angle CB-CA-HA, observed: 95.999, delta from target: 13.001
   A  79  LYS  HA , Angle N-CA-HA, observed: 95.960, delta from target: 14.040
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.750, delta from target: 16.250
   A  89  TYR  HA , Angle C-CA-HA, observed: 92.596, delta from target: 16.404
   A  89  TYR  HA , Angle CB-CA-HA, observed: 91.473, delta from target: 17.527
   A  79  LYS  HA , Angle C-CA-HA, observed: 127.369, delta from target: -18.369

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.105   2242  Z= 0.592
    Angle     :  2.302  25.564   4079  Z= 1.037
    Chirality :  1.000   5.586    176
    Planarity :  0.017   0.169    327
    Dihedral  : 14.888 110.358    769
    Min Nonbonded Distance : 1.466
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  :  7.30 %
      Favored  : 86.86 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  1.61 %
      Favored  : 91.13 %
    Cbeta Deviations :  7.58 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 9.92 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.92 (0.68), residues: 137
    helix: -2.06 (0.46), residues: 82
    sheet:  None (None), residues: 0
    loop : -1.48 (0.99), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.061   0.015   PHE A  15 
   TYR   0.379   0.032   TYR A  91 
   ARG   0.066   0.012   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.041   0.012   PHE A  15 
   TYR   0.244   0.034   TYR A  91 
   ARG   0.002   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   5.11 %
                favored =  80.29 %
  Rotamer outliers      =  22.58 %
  C-beta deviations     =     0
  Clashscore            =  18.49
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.53

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.047 (Z=  3.386)
  Mean delta:    0.013 (Z=  0.659)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   130.03    -8.33  1.80e+00  2.14e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.13     4.47  1.00e+00  2.00e+01   4.5*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    8.329 (Z=  4.627)
  Mean delta:    1.828 (Z=  1.015)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00  -139.65   -40.35  5.00e+00  6.51e+01   8.1*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   157.71    22.29  5.00e+00  1.99e+01   4.5*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -158.70   -21.30  5.00e+00  1.81e+01   4.3*sigma

  Min. delta:    0.023
  Max. delta:   88.856
  Mean delta:   17.096

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -1.60     4.11  2.00e-01  4.23e+02  20.6*sigma

  Min. delta:    0.001
  Max. delta:    4.113
  Mean delta:    0.324

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.048       0.089       46.42   4.4*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.109       0.088      238.44   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.109
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.047   2242  Z= 0.469
    Angle     :  1.702  11.470   4079  Z= 0.756
    Chirality :  0.324   4.113    176
    Planarity :  0.013   0.103    327
    Dihedral  : 14.330  88.856    769
    Min Nonbonded Distance : 1.830
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  8.03 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  3.23 %
      Favored  : 92.74 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.27 (0.61), residues: 137
    helix: -1.11 (0.49), residues: 74
    sheet:  None (None), residues: 0
    loop : -1.94 (0.74), residues: 63
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A 134 
   PHE   0.056   0.015   PHE A  67 
   TYR   0.225   0.029   TYR A  50 
   ARG   0.080   0.018   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A 134 
   PHE   0.037   0.016   PHE A  67 
   TYR   0.186   0.032   TYR A  50 
   ARG   0.010   0.003   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   8.03 %
                favored =  81.75 %
  Rotamer outliers      =   9.68 %
  C-beta deviations     =    13
  Clashscore            =  14.88
  RMS(bonds)            =   0.0114
  RMS(angles)           =   2.72
  MolProbity score      =   3.14

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   5.84 %
                favored =  86.86 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    10
  Clashscore            =  11.27
  RMS(bonds)            =   0.0114
  RMS(angles)           =   2.30
  MolProbity score      =   2.85

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Ramachandran outliers =   0.73 %
                favored =  91.24 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     1
  Clashscore            =   0.90
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.70
  MolProbity score      =   1.75

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.57    -0.12  1.60e-02  5.60e+01   7.5*sigma
   A  93  LEU  CA
   A  93  LEU  CB          1.53     1.63    -0.10  2.00e-02  2.64e+01   5.1*sigma
   A  92  THR  CA
   A  92  THR  C           1.52     1.43     0.09  2.10e-02  2.04e+01   4.5*sigma
   A  94  GLY  C
   A  95  ASP  N           1.33     1.27     0.06  1.40e-02  1.98e+01   4.5*sigma
   A  93  LEU  N
   A  93  LEU  CA          1.46     1.38     0.08  1.90e-02  1.88e+01   4.3*sigma
   A  93  LEU  C
   A  94  GLY  N           1.33     1.27     0.06  1.40e-02  1.76e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.120 (Z=  7.483)
  Mean delta:    0.017 (Z=  0.887)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    84.83    25.27  1.90e+00  1.77e+02  13.3*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    90.27    19.83  1.90e+00  1.09e+02  10.4*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   134.65   -23.35  2.30e+00  1.03e+02  10.2*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N         116.20    98.41    17.79  2.00e+00  7.91e+01   8.9*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50    96.43    14.07  1.70e+00  6.85e+01   8.3*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   136.53   -14.83  1.80e+00  6.79e+01   8.2*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  C         111.00   133.78   -22.78  2.80e+00  6.62e+01   8.1*sigma
   A  22  PRO  C
   A  22  PRO  CA
   A  22  PRO  CB        110.10   125.49   -15.39  1.90e+00  6.56e+01   8.1*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   107.47    14.23  1.80e+00  6.25e+01   7.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.12   -11.22  1.50e+00  5.59e+01   7.5*sigma
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        121.70   134.69   -12.99  1.80e+00  5.21e+01   7.2*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   109.87    11.83  1.80e+00  4.32e+01   6.6*sigma
   A  94  GLY  O
   A  94  GLY  C
   A  95  ASP  N         123.00   132.74    -9.74  1.60e+00  3.70e+01   6.1*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   110.77    10.93  1.80e+00  3.69e+01   6.1*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   120.68   -10.18  1.70e+00  3.58e+01   6.0*sigma
   A  22  PRO  CA
   A  22  PRO  CB
   A  22  PRO  CG        104.50    93.55    10.95  1.90e+00  3.32e+01   5.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   123.08   -11.48  2.00e+00  3.30e+01   5.7*sigma
   A 114  PRO  N
   A 114  PRO  CA
   A 114  PRO  CB        103.00   109.29    -6.29  1.10e+00  3.27e+01   5.7*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   108.13     5.67  1.00e+00  3.22e+01   5.7*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00   126.83   -15.83  2.80e+00  3.20e+01   5.7*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   120.66   -10.56  1.90e+00  3.09e+01   5.6*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   122.59   -10.99  2.00e+00  3.02e+01   5.5*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  C         111.00   126.34   -15.34  2.80e+00  3.00e+01   5.5*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   119.50    -9.10  1.70e+00  2.86e+01   5.4*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   105.60    10.60  2.00e+00  2.81e+01   5.3*sigma
   A 113  LYS  C
   A 113  LYS  CA
   A 113  LYS  CB        110.10   119.89    -9.79  1.90e+00  2.66e+01   5.2*sigma
   A 136  HIS  CA
   A 136  HIS  CB
   A 136  HIS  CG        113.80   118.89    -5.09  1.00e+00  2.59e+01   5.1*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.55     5.05  1.00e+00  2.55e+01   5.1*sigma
   A  22  PRO  CA
   A  22  PRO  N
   A  22  PRO  CD        112.00   105.05     6.95  1.40e+00  2.47e+01   5.0*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  C         111.00   124.83   -13.83  2.80e+00  2.44e+01   4.9*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   115.10     7.90  1.60e+00  2.44e+01   4.9*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   102.15     8.35  1.70e+00  2.42e+01   4.9*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   118.70    -4.90  1.00e+00  2.40e+01   4.9*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   119.09    -8.99  1.90e+00  2.24e+01   4.7*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   118.36    -7.86  1.70e+00  2.14e+01   4.6*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   117.15    -4.55  1.00e+00  2.07e+01   4.6*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   122.08    -8.18  1.80e+00  2.06e+01   4.5*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   129.80    -8.10  1.80e+00  2.03e+01   4.5*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N         116.90   123.44    -6.54  1.50e+00  1.90e+01   4.4*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10   118.17    -8.07  1.90e+00  1.80e+01   4.2*sigma
   A  70  LEU  C
   A  70  LEU  CA
   A  70  LEU  CB        110.10   118.04    -7.94  1.90e+00  1.75e+01   4.2*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   129.22    -7.52  1.80e+00  1.74e+01   4.2*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.78     5.42  1.30e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  41  VAL  C
   A  42  GLY  N
   A  42  GLY  CA        121.70   129.18    -7.48  1.80e+00  1.73e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.77     7.03  1.70e+00  1.71e+01   4.1*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   129.13    -7.43  1.80e+00  1.70e+01   4.1*sigma
   A 113  LYS  N
   A 113  LYS  CA
   A 113  LYS  CB        110.50   103.49     7.01  1.70e+00  1.70e+01   4.1*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.87     5.33  1.30e+00  1.68e+01   4.1*sigma
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG1       110.40   117.32    -6.92  1.70e+00  1.65e+01   4.1*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00   122.38   -11.38  2.80e+00  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   25.271 (Z= 13.301)
  Mean delta:    3.057 (Z=  1.625)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   -72.25  -107.75  5.00e+00  4.64e+02  21.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -84.77   -95.23  5.00e+00  3.63e+02  19.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -86.52   -93.48  5.00e+00  3.50e+02  18.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -118.08   -61.92  5.00e+00  1.53e+02  12.4*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   119.25    60.75  5.00e+00  1.48e+02  12.1*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   129.60    50.40  5.00e+00  1.02e+02  10.1*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00  -133.57   -46.43  5.00e+00  8.62e+01   9.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   136.38    43.62  5.00e+00  7.61e+01   8.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   137.86    42.14  5.00e+00  7.10e+01   8.4*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -137.87   -42.13  5.00e+00  7.10e+01   8.4*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   140.47    39.53  5.00e+00  6.25e+01   7.9*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   141.49    38.51  5.00e+00  5.93e+01   7.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   142.43    37.57  5.00e+00  5.65e+01   7.5*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   146.26    33.74  5.00e+00  4.55e+01   6.7*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   146.29    33.71  5.00e+00  4.55e+01   6.7*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -146.85   -33.15  5.00e+00  4.40e+01   6.6*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   151.04    28.96  5.00e+00  3.35e+01   5.8*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   152.41    27.59  5.00e+00  3.05e+01   5.5*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   158.11    21.89  5.00e+00  1.92e+01   4.4*sigma
   A  22  PRO  CA
   A  22  PRO  C
   A  23  ASP  N
   A  23  ASP  CA        180.00   159.59    20.41  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.042
  Max. delta:  107.747
  Mean delta:   18.252

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.90     5.41  2.00e-01  7.31e+02  27.0*sigma
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51    -2.30     4.81  2.00e-01  5.79e+02  24.1*sigma
   A  22  PRO  CA
   A  22  PRO  N
   A  22  PRO  C
   A  22  PRO  CB          2.72    -1.82     4.54  2.00e-01  5.14e+02  22.7*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -1.67     4.18  2.00e-01  4.38e+02  20.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.26     3.69  2.00e-01  3.41e+02  18.5*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -0.84     3.35  2.00e-01  2.80e+02  16.7*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     0.16     2.35  2.00e-01  1.38e+02  11.7*sigma

  Min. delta:    0.001
  Max. delta:    5.407
  Mean delta:    0.839

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O
   A  91  TYR  N             0.048       0.084       23.37   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.125
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  86  ILE  HA , Angle N-CA-HA, observed: 96.769, delta from target: 13.231
   A  78  ILE  HB , Angle CA-CB-HB, observed: 95.506, delta from target: 13.494
   A  51  ILE  HA , Angle CB-CA-HA, observed: 94.552, delta from target: 14.448
   A  78  ILE  HA , Angle C-CA-HA, observed: 92.119, delta from target: 16.881
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.332, delta from target: 17.668
   A  90  SER  HA , Angle N-CA-HA, observed: 91.637, delta from target: 18.363
   A  22  PRO  HA , Angle C-CA-HA, observed: 90.056, delta from target: 18.944
   A  74  ASP  HA , Angle C-CA-HA, observed: 88.641, delta from target: 20.359
   A  79  LYS  HA , Angle CB-CA-HA, observed: 132.097, delta from target: -23.097
   A  89  TYR  HA , Angle C-CA-HA, observed: 82.816, delta from target: 26.184
   A  93  LEU  HA , Angle CB-CA-HA, observed: 141.255, delta from target: -32.255
   A  81  TYR  HA , Angle N-CA-HA, observed: 63.615, delta from target: 46.385

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.120   2242  Z= 0.632
    Angle     :  2.743  46.385   4079  Z= 1.200
    Chirality :  0.839   5.407    176
    Planarity :  0.015   0.125    327
    Dihedral  : 15.390 107.747    769
    Min Nonbonded Distance : 1.388
  
  Molprobity Statistics.
    All-atom Clashscore : 13.98
    Ramachandran Plot:
      Outliers :  9.49 %
      Allowed  :  8.76 %
      Favored  : 81.75 %
    Rotamer:
      Outliers : 11.29 %
      Allowed  :  4.84 %
      Favored  : 83.87 %
    Cbeta Deviations :  9.09 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 12.21 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.69 (0.56), residues: 137
    helix: -2.85 (0.42), residues: 72
    sheet:  None (None), residues: 0
    loop : -3.42 (0.69), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.005   HIS A 138 
   PHE   0.134   0.019   PHE A  67 
   TYR   0.104   0.018   TYR A 111 
   ARG   0.076   0.014   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.005   HIS A 138 
   PHE   0.061   0.011   PHE A  67 
   TYR   0.086   0.020   TYR A 111 
   ARG   0.005   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.045 (Z=  3.480)
  Mean delta:    0.013 (Z=  0.666)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 119  LEU  N
   A 119  LEU  CA
   A 119  LEU  C         111.00   128.09   -17.09  2.80e+00  3.72e+01   6.1*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N         116.20   126.90   -10.70  2.00e+00  2.86e+01   5.4*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.88    -5.28  1.00e+00  2.78e+01   5.3*sigma
   A  41  VAL  CA
   A  41  VAL  CB
   A  41  VAL  CG1       110.40   118.98    -8.58  1.70e+00  2.55e+01   5.0*sigma
   A  85  LYS  CA
   A  85  LYS  CB
   A  85  LYS  CG        114.10   124.18   -10.08  2.00e+00  2.54e+01   5.0*sigma
   A 129  ARG  C
   A 129  ARG  CA
   A 129  ARG  CB        110.10   119.36    -9.26  1.90e+00  2.37e+01   4.9*sigma
   A 137  HIS  CA
   A 137  HIS  CB
   A 137  HIS  CG        113.80   118.24    -4.44  1.00e+00  1.97e+01   4.4*sigma
   A  85  LYS  CB
   A  85  LYS  CG
   A  85  LYS  CD        111.30   121.27    -9.97  2.30e+00  1.88e+01   4.3*sigma
   A 119  LEU  O
   A 119  LEU  C
   A 120  GLU  N         123.00   116.11     6.89  1.60e+00  1.86e+01   4.3*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   129.34    -7.64  1.80e+00  1.80e+01   4.2*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.86     5.34  1.30e+00  1.68e+01   4.1*sigma
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        121.70   128.93    -7.23  1.80e+00  1.62e+01   4.0*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   116.61    -4.01  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   17.088 (Z=  6.103)
  Mean delta:    2.170 (Z=  1.182)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00  -136.44   -43.56  5.00e+00  7.59e+01   8.7*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00  -146.70   -33.30  5.00e+00  4.43e+01   6.7*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   150.64    29.36  5.00e+00  3.45e+01   5.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   156.46    23.54  5.00e+00  2.22e+01   4.7*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   159.75    20.25  5.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.040
  Max. delta:   89.882
  Mean delta:   20.789

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.06     4.57  2.00e-01  5.23e+02  22.9*sigma
   A 120  GLU  CA
   A 120  GLU  N
   A 120  GLU  C
   A 120  GLU  CB          2.51    -1.97     4.49  2.00e-01  5.03e+02  22.4*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -1.69     4.20  2.00e-01  4.41e+02  21.0*sigma
   A 129  ARG  CA
   A 129  ARG  N
   A 129  ARG  C
   A 129  ARG  CB          2.51     1.40     1.11  2.00e-01  3.07e+01   5.5*sigma

  Min. delta:    0.001
  Max. delta:    4.575
  Mean delta:    0.593

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.066       0.125       87.86   6.3*sigma

  Min. delta:    0.000
  Max. delta:    0.130
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 129  ARG  HA , Angle C-CA-HA, observed: 96.052, delta from target: 12.948
   A 120  GLU  HA , Angle C-CA-HA, observed: 95.833, delta from target: 13.167
   A 119  LEU  HG , Angle CD1-CG-HG, observed: 94.709, delta from target: 13.291
   A 119  LEU  HA , Angle C-CA-HA, observed: 94.437, delta from target: 14.563
   A 119  LEU  HA , Angle N-CA-HA, observed: 92.054, delta from target: 17.946

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.045   2242  Z= 0.474
    Angle     :  1.954  17.946   4079  Z= 0.869
    Chirality :  0.593   4.575    176
    Planarity :  0.013   0.095    327
    Dihedral  : 16.811  89.882    769
    Min Nonbonded Distance : 1.504
  
  Molprobity Statistics.
    All-atom Clashscore : 11.72
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  : 10.95 %
      Favored  : 88.32 %
    Rotamer:
      Outliers : 10.48 %
      Allowed  : 10.48 %
      Favored  : 79.03 %
    Cbeta Deviations :  3.79 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 1.53 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.65 (0.70), residues: 137
    helix: -0.79 (0.57), residues: 69
    sheet:  None (None), residues: 0
    loop : -1.35 (0.81), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.004   HIS A  43 
   PHE   0.101   0.024   PHE A  67 
   TYR   0.160   0.022   TYR A 111 
   ARG   0.095   0.015   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.004   HIS A  43 
   PHE   0.070   0.023   PHE A  67 
   TYR   0.125   0.020   TYR A 111 
   ARG   0.020   0.005   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.73 %
                favored =  88.32 %
  Rotamer outliers      =  10.48 %
  C-beta deviations     =     5
  Clashscore            =  11.72
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.95
  MolProbity score      =   2.95

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   9.49 %
                favored =  81.75 %
  Rotamer outliers      =  11.29 %
  C-beta deviations     =    12
  Clashscore            =  13.98
  RMS(bonds)            =   0.0122
  RMS(angles)           =   2.74
  MolProbity score      =   3.16

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.838, 43.477, 60.042, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.67    -0.15  2.10e-02  4.90e+01   7.0*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.57    -0.11  1.90e-02  3.55e+01   6.0*sigma
   A 129  ARG  C
   A 130  SER  N           1.33     1.41    -0.08  1.40e-02  3.51e+01   5.9*sigma
   A  87  GLY  CA
   A  87  GLY  C           1.52     1.60    -0.09  1.80e-02  2.30e+01   4.8*sigma
   A  88  ASP  N
   A  88  ASP  CA          1.46     1.54    -0.08  1.90e-02  1.72e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.147 (Z=  7.003)
  Mean delta:    0.017 (Z=  0.878)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   137.16   -27.06  1.90e+00  2.03e+02  14.2*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30   136.19   -26.89  2.00e+00  1.81e+02  13.4*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    76.26    34.74  2.80e+00  1.54e+02  12.4*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   139.63   -17.93  1.80e+00  9.92e+01  10.0*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    94.65    15.85  1.70e+00  8.70e+01   9.3*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  CB        110.50    94.85    15.65  1.70e+00  8.47e+01   9.2*sigma
   A  77  ILE  O
   A  77  ILE  C
   A  78  ILE  N         123.00   109.06    13.94  1.60e+00  7.59e+01   8.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   137.13   -15.43  1.80e+00  7.35e+01   8.6*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   130.76   -19.46  2.30e+00  7.16e+01   8.5*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  C         111.00   133.77   -22.77  2.80e+00  6.61e+01   8.1*sigma
   A  80  GLY  N
   A  80  GLY  CA
   A  80  GLY  C         113.30    91.29    22.01  2.90e+00  5.76e+01   7.6*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   134.90   -13.20  1.80e+00  5.37e+01   7.3*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  CB        111.50   123.79   -12.29  1.70e+00  5.22e+01   7.2*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   119.78    -7.18  1.00e+00  5.15e+01   7.2*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   133.91   -12.21  1.80e+00  4.60e+01   6.8*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   133.60   -11.90  1.80e+00  4.37e+01   6.6*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   132.74   -11.04  1.80e+00  3.76e+01   6.1*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   100.43     9.17  1.50e+00  3.74e+01   6.1*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.60   -10.90  1.80e+00  3.66e+01   6.1*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   132.43   -10.73  1.80e+00  3.55e+01   6.0*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   104.44    11.76  2.00e+00  3.46e+01   5.9*sigma
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        121.70   132.14   -10.44  1.80e+00  3.37e+01   5.8*sigma
   A 128  MET  O
   A 128  MET  C
   A 129  ARG  N         123.00   114.02     8.98  1.60e+00  3.15e+01   5.6*sigma
   A  88  ASP  O
   A  88  ASP  C
   A  89  TYR  N         123.00   114.13     8.87  1.60e+00  3.07e+01   5.5*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   104.50     7.50  1.40e+00  2.87e+01   5.4*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00   125.95   -14.95  2.80e+00  2.85e+01   5.3*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   126.80   -10.60  2.00e+00  2.81e+01   5.3*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   119.96    -9.86  1.90e+00  2.69e+01   5.2*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   117.53    -4.93  1.00e+00  2.43e+01   4.9*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.46    -9.86  2.00e+00  2.43e+01   4.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.35    -4.75  1.00e+00  2.25e+01   4.7*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   113.33     8.37  1.80e+00  2.16e+01   4.7*sigma
   A 129  ARG  C
   A 129  ARG  CA
   A 129  ARG  CB        110.10   118.93    -8.83  1.90e+00  2.16e+01   4.6*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   123.43   -12.43  2.80e+00  1.97e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.44     5.76  1.30e+00  1.96e+01   4.4*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  C         111.00   123.38   -12.38  2.80e+00  1.95e+01   4.4*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   115.96     7.04  1.60e+00  1.93e+01   4.4*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   129.42    -7.72  1.80e+00  1.84e+01   4.3*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   124.76    -8.56  2.00e+00  1.83e+01   4.3*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   104.23     7.27  1.70e+00  1.83e+01   4.3*sigma
   A 127  ARG  O
   A 127  ARG  C
   A 128  MET  N         123.00   129.78    -6.78  1.60e+00  1.80e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.76e+01   4.2*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   107.61    -4.61  1.10e+00  1.75e+01   4.2*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG2       110.50   117.60    -7.10  1.70e+00  1.75e+01   4.2*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.78     5.42  1.30e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.45     4.15  1.00e+00  1.72e+01   4.1*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N         116.20   124.46    -8.26  2.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   34.744 (Z= 14.240)
  Mean delta:    3.222 (Z=  1.667)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -51.22  -128.78  5.00e+00  6.63e+02  25.8*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -55.69  -124.31  5.00e+00  6.18e+02  24.9*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00    67.97   112.03  5.00e+00  5.02e+02  22.4*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    89.53    90.47  5.00e+00  3.27e+02  18.1*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00  -109.64   -70.36  5.00e+00  1.98e+02  14.1*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -112.53   -67.47  5.00e+00  1.82e+02  13.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -122.58   -57.42  5.00e+00  1.32e+02  11.5*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -129.63   -50.37  5.00e+00  1.01e+02  10.1*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   133.46    46.54  5.00e+00  8.66e+01   9.3*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   134.41    45.59  5.00e+00  8.31e+01   9.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   135.98    44.02  5.00e+00  7.75e+01   8.8*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   138.52    41.48  5.00e+00  6.88e+01   8.3*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   139.30    40.70  5.00e+00  6.63e+01   8.1*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   139.88    40.12  5.00e+00  6.44e+01   8.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   140.89    39.11  5.00e+00  6.12e+01   7.8*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   140.92    39.08  5.00e+00  6.11e+01   7.8*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -141.59   -38.41  5.00e+00  5.90e+01   7.7*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   143.55    36.45  5.00e+00  5.31e+01   7.3*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -143.98   -36.02  5.00e+00  5.19e+01   7.2*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA          0.00    35.92   -35.92  5.00e+00  5.16e+01   7.2*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   144.36    35.64  5.00e+00  5.08e+01   7.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -149.50   -30.50  5.00e+00  3.72e+01   6.1*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   155.39    24.61  5.00e+00  2.42e+01   4.9*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   159.89    20.11  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.016
  Max. delta:  128.777
  Mean delta:   20.788

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -3.23     5.88  2.00e-01  8.64e+02  29.4*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.63     5.15  2.00e-01  6.63e+02  25.8*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.60     5.11  2.00e-01  6.54e+02  25.6*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.46     4.97  2.00e-01  6.18e+02  24.9*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -2.06     4.57  2.00e-01  5.22e+02  22.8*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.97     4.41  2.00e-01  4.86e+02  22.0*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -1.73     4.24  2.00e-01  4.50e+02  21.2*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.25     3.69  2.00e-01  3.40e+02  18.4*sigma
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51     1.65     0.86  2.00e-01  1.86e+01   4.3*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55     1.72     0.83  2.00e-01  1.74e+01   4.2*sigma

  Min. delta:    0.001
  Max. delta:    5.878
  Mean delta:    1.038

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.141
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  90  SER  HA , Angle C-CA-HA, observed: 96.525, delta from target: 12.475
   A  79  LYS  HA , Angle CB-CA-HA, observed: 127.703, delta from target: -18.703
   A  88  ASP  HA , Angle CB-CA-HA, observed: 128.309, delta from target: -19.309
   A  78  ILE  HA , Angle CB-CA-HA, observed: 87.985, delta from target: 21.015
   A  92  THR  HB , Angle CG2-CB-HB, observed: 85.960, delta from target: 22.040
   A  92  THR  HB , Angle CA-CB-HB, observed: 131.975, delta from target: -22.975
   A  88  ASP  HA , Angle N-CA-HA, observed: 80.630, delta from target: 29.370
   A 128  MET  HA , Angle N-CA-HA, observed: 148.228, delta from target: -38.228

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.147   2242  Z= 0.625
    Angle     :  2.787  38.228   4079  Z= 1.215
    Chirality :  1.038   5.878    176
    Planarity :  0.015   0.141    327
    Dihedral  : 16.966 128.777    769
    Min Nonbonded Distance : 1.563
  
  Molprobity Statistics.
    All-atom Clashscore : 17.58
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  : 13.14 %
      Favored  : 81.02 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  4.84 %
      Favored  : 87.90 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 28.57 %
      Twisted General : 15.27 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.74 (0.65), residues: 137
    helix: -2.09 (0.53), residues: 68
    sheet:  None (None), residues: 0
    loop : -2.93 (0.75), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A  43 
   PHE   0.068   0.015   PHE A  45 
   TYR   0.222   0.024   TYR A  50 
   ARG   0.039   0.009   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A  43 
   PHE   0.048   0.015   PHE A  45 
   TYR   0.180   0.029   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 128  MET  N
   A 128  MET  CA          1.46     1.56    -0.11  1.90e-02  3.15e+01   5.6*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.40    -0.07  1.40e-02  2.70e+01   5.2*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.55    -0.10  1.90e-02  2.60e+01   5.1*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.62    -0.10  2.10e-02  2.20e+01   4.7*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.107 (Z=  5.614)
  Mean delta:    0.016 (Z=  0.812)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N         116.20   101.44    14.76  2.00e+00  5.44e+01   7.4*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   134.55   -12.85  1.80e+00  5.10e+01   7.1*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   125.09   -13.49  2.00e+00  4.55e+01   6.7*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   124.29   -12.69  2.00e+00  4.02e+01   6.3*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   132.61   -10.91  1.80e+00  3.67e+01   6.1*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00   127.44   -16.44  2.80e+00  3.45e+01   5.9*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   102.09     9.41  1.70e+00  3.07e+01   5.5*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   119.64    -9.14  1.70e+00  2.89e+01   5.4*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   131.05    -9.35  1.80e+00  2.70e+01   5.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   124.51    -7.61  1.50e+00  2.57e+01   5.1*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.66    -5.06  1.00e+00  2.56e+01   5.1*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   106.14    10.06  2.00e+00  2.53e+01   5.0*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   119.98    -8.48  1.70e+00  2.49e+01   5.0*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00   124.96   -13.96  2.80e+00  2.49e+01   5.0*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   124.78     6.42  1.30e+00  2.44e+01   4.9*sigma
   A 124  ALA  O
   A 124  ALA  C
   A 125  LYS  N         123.00   130.86    -7.86  1.60e+00  2.41e+01   4.9*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG1       110.40   118.70    -8.30  1.70e+00  2.38e+01   4.9*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   130.44    -8.74  1.80e+00  2.36e+01   4.9*sigma
   A  83  THR  N
   A  83  THR  CA
   A  83  THR  CB        111.50   103.29     8.21  1.70e+00  2.33e+01   4.8*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   119.03    -8.93  1.90e+00  2.21e+01   4.7*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   130.10    -8.40  1.80e+00  2.18e+01   4.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   130.06    -8.36  1.80e+00  2.16e+01   4.6*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   118.31    -7.81  1.70e+00  2.11e+01   4.6*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   118.17    -7.67  1.70e+00  2.04e+01   4.5*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   118.27    -4.47  1.00e+00  2.00e+01   4.5*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  CB        110.50   118.10    -7.60  1.70e+00  2.00e+01   4.5*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    98.53    12.47  2.80e+00  1.98e+01   4.5*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   120.36    -8.76  2.00e+00  1.92e+01   4.4*sigma
   A  83  THR  OG1
   A  83  THR  CB
   A  83  THR  CG2       109.30   100.57     8.73  2.00e+00  1.91e+01   4.4*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   129.49    -7.79  1.80e+00  1.87e+01   4.3*sigma
   A  39  LEU  N
   A  39  LEU  CA
   A  39  LEU  CB        110.50   103.20     7.30  1.70e+00  1.84e+01   4.3*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   103.21     7.29  1.70e+00  1.84e+01   4.3*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   117.59    -7.19  1.70e+00  1.79e+01   4.2*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N         116.20   107.91     8.29  2.00e+00  1.72e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O         120.80   127.67    -6.87  1.70e+00  1.64e+01   4.0*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.56     4.04  1.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   16.442 (Z=  7.378)
  Mean delta:    2.597 (Z=  1.402)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    53.46   126.54  5.00e+00  6.40e+02  25.3*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   115.90    64.10  5.00e+00  1.64e+02  12.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   123.67    56.33  5.00e+00  1.27e+02  11.3*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -125.47   -54.53  5.00e+00  1.19e+02  10.9*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   130.01    49.99  5.00e+00  1.00e+02  10.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -130.87   -49.13  5.00e+00  9.66e+01   9.8*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   134.83    45.17  5.00e+00  8.16e+01   9.0*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   138.31    41.69  5.00e+00  6.95e+01   8.3*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   143.81    36.19  5.00e+00  5.24e+01   7.2*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   147.75    32.25  5.00e+00  4.16e+01   6.4*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   152.16    27.84  5.00e+00  3.10e+01   5.6*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   153.78    26.22  5.00e+00  2.75e+01   5.2*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -156.08   -23.92  5.00e+00  2.29e+01   4.8*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   156.26    23.74  5.00e+00  2.25e+01   4.7*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   156.52    23.48  5.00e+00  2.21e+01   4.7*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00  -158.00   -22.00  5.00e+00  1.94e+01   4.4*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -158.62   -21.38  5.00e+00  1.83e+01   4.3*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   158.73    21.27  5.00e+00  1.81e+01   4.3*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   159.19    20.81  5.00e+00  1.73e+01   4.2*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   159.29    20.71  5.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.022
  Max. delta:  126.538
  Mean delta:   17.415

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.11     5.62  2.00e-01  7.91e+02  28.1*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.64     5.29  2.00e-01  6.98e+02  26.4*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.28     4.93  2.00e-01  6.07e+02  24.6*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.37     4.88  2.00e-01  5.97e+02  24.4*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.39     4.83  2.00e-01  5.83e+02  24.1*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.27     4.78  2.00e-01  5.71e+02  23.9*sigma
   A 129  ARG  CA
   A 129  ARG  N
   A 129  ARG  C
   A 129  ARG  CB          2.51    -1.87     4.38  2.00e-01  4.80e+02  21.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.74     3.17  2.00e-01  2.52e+02  15.9*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43     0.82     1.61  2.00e-01  6.50e+01   8.1*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51     1.61     0.90  2.00e-01  2.03e+01   4.5*sigma

  Min. delta:    0.000
  Max. delta:    5.624
  Mean delta:    1.041

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.053       0.105       56.40   5.2*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.043       0.082       37.74   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.053
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    3" pdbres="HIS A  43  conformer  : HE2, HD1 
    3" pdbres="HIS A 134  conformer  : HE2, HD1 
    3" pdbres="HIS A 135  conformer  : HE2, HD1 
    3" pdbres="HIS A 136  conformer  : HE2, HD1 
    3" pdbres="HIS A 137  conformer  : HE2, HD1 
    3" pdbres="HIS A 138  conformer  : HE2, HD1 
    3" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 128  MET  HA , Angle CB-CA-HA, observed: 121.302, delta from target: -12.302
   A 126  VAL  HA , Angle N-CA-HA, observed: 95.990, delta from target: 14.010
   A  78  ILE  HA , Angle CB-CA-HA, observed: 94.920, delta from target: 14.080
   A  51  ILE  HA , Angle C-CA-HA, observed: 87.353, delta from target: 21.647
   A  51  ILE  HA , Angle CB-CA-HA, observed: 83.225, delta from target: 25.775
   A  77  ILE  HA , Angle C-CA-HA, observed: 68.567, delta from target: 40.433

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.107   2242  Z= 0.578
    Angle     :  2.423  40.433   4079  Z= 1.054
    Chirality :  1.041   5.624    176
    Planarity :  0.010   0.051    327
    Dihedral  : 14.384 126.538    769
    Min Nonbonded Distance : 1.629
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  5.11 %
      Allowed  : 15.33 %
      Favored  : 79.56 %
    Rotamer:
      Outliers :  8.06 %
      Allowed  :  4.84 %
      Favored  : 87.10 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 7.63 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.17 (0.58), residues: 137
    helix: -1.74 (0.54), residues: 63
    sheet:  None (None), residues: 0
    loop : -3.89 (0.58), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.060   0.017   PHE A  15 
   TYR   0.135   0.019   TYR A  89 
   ARG   0.022   0.005   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.040   0.016   PHE A  15 
   TYR   0.105   0.023   TYR A  89 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.56    -0.11  1.60e-02  4.42e+01   6.6*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.25     0.08  1.40e-02  2.98e+01   5.5*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.62    -0.09  2.10e-02  2.05e+01   4.5*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.106 (Z=  6.649)
  Mean delta:    0.016 (Z=  0.849)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   101.34    20.36  1.80e+00  1.28e+02  11.3*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   140.21   -29.21  2.80e+00  1.09e+02  10.4*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   125.98   -15.48  1.70e+00  8.29e+01   9.1*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60    93.56    18.04  2.00e+00  8.14e+01   9.0*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   125.04   -14.54  1.70e+00  7.31e+01   8.6*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   127.18   -15.78  1.90e+00  6.90e+01   8.3*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   123.81   -13.31  1.70e+00  6.13e+01   7.8*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   110.88    12.12  1.60e+00  5.74e+01   7.6*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   135.27   -13.57  1.80e+00  5.69e+01   7.5*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    90.81    20.19  2.80e+00  5.20e+01   7.2*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   122.56   -12.16  1.70e+00  5.12e+01   7.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   130.49   -14.29  2.00e+00  5.10e+01   7.1*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   109.42    12.28  1.80e+00  4.65e+01   6.8*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   125.95   -12.05  1.80e+00  4.48e+01   6.7*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    99.32    11.18  1.70e+00  4.33e+01   6.6*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   103.06    13.14  2.00e+00  4.32e+01   6.6*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   129.37   -18.37  2.80e+00  4.30e+01   6.6*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   122.16   -12.06  1.90e+00  4.03e+01   6.3*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   121.24   -10.74  1.70e+00  3.99e+01   6.3*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   132.84   -11.14  1.80e+00  3.83e+01   6.2*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00    95.22    15.78  2.80e+00  3.18e+01   5.6*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   125.08   -10.98  2.00e+00  3.01e+01   5.5*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.00    -5.40  1.00e+00  2.92e+01   5.4*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10   119.89    -9.79  1.90e+00  2.66e+01   5.2*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    96.58    14.42  2.80e+00  2.65e+01   5.2*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   100.35     9.75  1.90e+00  2.63e+01   5.1*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   130.63    -8.93  1.80e+00  2.46e+01   5.0*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   102.43     7.17  1.50e+00  2.29e+01   4.8*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   103.57     7.93  1.70e+00  2.18e+01   4.7*sigma
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        121.70   130.00    -8.30  1.80e+00  2.13e+01   4.6*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30   100.13     9.17  2.00e+00  2.10e+01   4.6*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   117.18    -4.58  1.00e+00  2.10e+01   4.6*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   129.88    -8.18  1.80e+00  2.07e+01   4.5*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   118.13    -7.63  1.70e+00  2.02e+01   4.5*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   118.56    -8.46  1.90e+00  1.98e+01   4.5*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG1       110.40   117.89    -7.49  1.70e+00  1.94e+01   4.4*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   129.57    -7.87  1.80e+00  1.91e+01   4.4*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   123.16   -12.16  2.80e+00  1.89e+01   4.3*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   129.24    -7.54  1.80e+00  1.75e+01   4.2*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   121.44    -7.54  1.80e+00  1.75e+01   4.2*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   127.77    -6.97  1.70e+00  1.68e+01   4.1*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   108.02     8.18  2.00e+00  1.67e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.63e+01   4.0*sigma
   A  22  PRO  N
   A  22  PRO  CA
   A  22  PRO  CB        103.00   107.42    -4.42  1.10e+00  1.62e+01   4.0*sigma
   A  83  THR  C
   A  83  THR  CA
   A  83  THR  CB        109.10   100.28     8.82  2.20e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   29.206 (Z= 11.312)
  Mean delta:    2.972 (Z=  1.548)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00    97.66    82.34  5.00e+00  2.71e+02  16.5*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   103.67    76.33  5.00e+00  2.33e+02  15.3*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   106.09    73.91  5.00e+00  2.19e+02  14.8*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -106.40   -73.60  5.00e+00  2.17e+02  14.7*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   114.27    65.73  5.00e+00  1.73e+02  13.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -117.90   -62.10  5.00e+00  1.54e+02  12.4*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   118.65    61.35  5.00e+00  1.51e+02  12.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   123.88    56.12  5.00e+00  1.26e+02  11.2*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   129.48    50.52  5.00e+00  1.02e+02  10.1*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -133.51   -46.49  5.00e+00  8.65e+01   9.3*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   136.09    43.91  5.00e+00  7.71e+01   8.8*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -138.84   -41.16  5.00e+00  6.78e+01   8.2*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -138.85   -41.15  5.00e+00  6.77e+01   8.2*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   142.04    37.96  5.00e+00  5.76e+01   7.6*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   143.86    36.14  5.00e+00  5.22e+01   7.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA          0.00   -31.29    31.29  5.00e+00  3.92e+01   6.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   152.87    27.13  5.00e+00  2.94e+01   5.4*sigma
   A  70  LEU  CA
   A  70  LEU  C
   A  71  ILE  N
   A  71  ILE  CA        180.00   153.16    26.84  5.00e+00  2.88e+01   5.4*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -153.24   -26.76  5.00e+00  2.86e+01   5.4*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -154.31   -25.69  5.00e+00  2.64e+01   5.1*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   154.44    25.56  5.00e+00  2.61e+01   5.1*sigma
   A  53  LEU  CA
   A  53  LEU  C
   A  54  PRO  N
   A  54  PRO  CA        180.00   155.91    24.09  5.00e+00  2.32e+01   4.8*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -159.26   -20.74  5.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.060
  Max. delta:   88.941
  Mean delta:   17.780

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.58     5.02  2.00e-01  6.31e+02  25.1*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.21     4.85  2.00e-01  5.88e+02  24.3*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.26     4.79  2.00e-01  5.73e+02  23.9*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.31     4.74  2.00e-01  5.62e+02  23.7*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51    -0.63     3.14  2.00e-01  2.47e+02  15.7*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     1.56     0.95  2.00e-01  2.27e+01   4.8*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     1.66     0.85  2.00e-01  1.81e+01   4.3*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51     1.69     0.82  2.00e-01  1.67e+01   4.1*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51     3.31    -0.80  2.00e-01  1.61e+01   4.0*sigma

  Min. delta:    0.000
  Max. delta:    5.022
  Mean delta:    0.796

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.089       0.122      159.61   6.1*sigma
   A 128  MET  CA
   A 128  MET  C
   A 128  MET  O
   A 129  ARG  N             0.062       0.107       38.05   5.3*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.048       0.092       46.29   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.089
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 127  ARG  HA , Angle C-CA-HA, observed: 96.909, delta from target: 12.091
   A  92  THR  HB , Angle OG1-CB-HB, observed: 121.102, delta from target: -12.102
   A 127  ARG  HA , Angle N-CA-HA, observed: 97.744, delta from target: 12.256
   A  97  SER  HA , Angle CB-CA-HA, observed: 95.853, delta from target: 13.147
   A  79  LYS  HA , Angle N-CA-HA, observed: 124.394, delta from target: -14.394
   A  89  TYR  HA , Angle C-CA-HA, observed: 94.458, delta from target: 14.542
   A 122  ILE  HA , Angle C-CA-HA, observed: 94.007, delta from target: 14.993
   A  90  SER  HA , Angle CB-CA-HA, observed: 92.703, delta from target: 16.297
   A  78  ILE  HB , Angle CA-CB-HB, observed: 92.108, delta from target: 16.892
   A  78  ILE  HA , Angle N-CA-HA, observed: 92.886, delta from target: 17.114
   A  81  TYR  HA , Angle CB-CA-HA, observed: 91.068, delta from target: 17.932
   A  91  TYR  HA , Angle N-CA-HA, observed: 91.449, delta from target: 18.551
   A  78  ILE  HA , Angle CB-CA-HA, observed: 129.019, delta from target: -20.019
   A 126  VAL  HA , Angle N-CA-HA, observed: 131.343, delta from target: -21.343
   A  89  TYR  HA , Angle N-CA-HA, observed: 81.842, delta from target: 28.158
   A  89  TYR  HA , Angle CB-CA-HA, observed: 137.335, delta from target: -28.335
   A  81  TYR  HA , Angle N-CA-HA, observed: 74.517, delta from target: 35.483

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.106   2242  Z= 0.604
    Angle     :  2.708  35.483   4079  Z= 1.162
    Chirality :  0.796   5.022    176
    Planarity :  0.013   0.125    327
    Dihedral  : 14.771  88.941    769
    Min Nonbonded Distance : 1.517
  
  Molprobity Statistics.
    All-atom Clashscore : 22.54
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  :  5.84 %
      Favored  : 87.59 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  4.03 %
      Favored  : 89.52 %
    Cbeta Deviations : 11.36 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 11.45 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.10 (0.67), residues: 137
    helix: -1.64 (0.56), residues: 62
    sheet:  None (None), residues: 0
    loop : -2.49 (0.74), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A 138 
   PHE   0.043   0.008   PHE A  45 
   TYR   0.230   0.030   TYR A  81 
   ARG   0.044   0.006   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A 138 
   PHE   0.032   0.009   PHE A  45 
   TYR   0.137   0.029   TYR A  81 
   ARG   0.001   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 129  ARG  N
   A 129  ARG  CA          1.46     1.60    -0.14  1.90e-02  5.23e+01   7.2*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.65    -0.13  2.10e-02  3.70e+01   6.1*sigma
   A  77  ILE  N
   A  77  ILE  CA          1.46     1.55    -0.09  1.90e-02  2.31e+01   4.8*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.55    -0.09  1.90e-02  2.31e+01   4.8*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.39    -0.06  1.40e-02  1.87e+01   4.3*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.54    -0.08  1.90e-02  1.73e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.137 (Z=  7.235)
  Mean delta:    0.017 (Z=  0.901)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   141.43   -19.73  1.80e+00  1.20e+02  11.0*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   137.04   -26.04  2.80e+00  8.65e+01   9.3*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   137.65   -15.95  1.80e+00  7.85e+01   8.9*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   126.58   -16.48  1.90e+00  7.53e+01   8.7*sigma
   A 125  LYS  C
   A 125  LYS  CA
   A 125  LYS  CB        110.10   125.94   -15.84  1.90e+00  6.95e+01   8.3*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    87.83    23.17  2.80e+00  6.85e+01   8.3*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    97.48    14.02  1.70e+00  6.80e+01   8.2*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   135.90   -14.20  1.80e+00  6.22e+01   7.9*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    90.19    20.81  2.80e+00  5.52e+01   7.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   135.04   -13.34  1.80e+00  5.49e+01   7.4*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   134.97   -13.27  1.80e+00  5.43e+01   7.4*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   130.56   -14.36  2.00e+00  5.15e+01   7.2*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   125.91   -14.31  2.00e+00  5.12e+01   7.2*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  C         111.00    91.25    19.75  2.80e+00  4.98e+01   7.1*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   129.87   -18.87  2.80e+00  4.54e+01   6.7*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   122.62   -11.12  1.70e+00  4.28e+01   6.5*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   121.46   -10.96  1.70e+00  4.16e+01   6.4*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50    99.79    10.71  1.70e+00  3.97e+01   6.3*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG2       110.50   121.00   -10.50  1.70e+00  3.81e+01   6.2*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   121.21   -11.11  1.90e+00  3.42e+01   5.8*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   131.82   -10.12  1.80e+00  3.16e+01   5.6*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   124.91   -10.81  2.00e+00  2.92e+01   5.4*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   114.43     8.57  1.60e+00  2.87e+01   5.4*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   123.52    -9.62  1.80e+00  2.86e+01   5.3*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.93    -5.33  1.00e+00  2.84e+01   5.3*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N         116.20   126.79   -10.59  2.00e+00  2.80e+01   5.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   124.70    -7.80  1.50e+00  2.71e+01   5.2*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   112.51     9.19  1.80e+00  2.61e+01   5.1*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.57    -4.97  1.00e+00  2.47e+01   5.0*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   112.90     8.80  1.80e+00  2.39e+01   4.9*sigma
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        121.70   130.37    -8.67  1.80e+00  2.32e+01   4.8*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00    97.63    13.37  2.80e+00  2.28e+01   4.8*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  C         111.00   124.33   -13.33  2.80e+00  2.27e+01   4.8*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   115.64     7.36  1.60e+00  2.11e+01   4.6*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   118.80    -8.70  1.90e+00  2.10e+01   4.6*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   125.00    -8.80  2.00e+00  1.94e+01   4.4*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   114.07     7.63  1.80e+00  1.80e+01   4.2*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   116.86    -6.36  1.50e+00  1.80e+01   4.2*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N         116.20   107.76     8.44  2.00e+00  1.78e+01   4.2*sigma
   A 102  PRO  N
   A 102  PRO  CA
   A 102  PRO  CB        103.00   107.63    -4.63  1.10e+00  1.77e+01   4.2*sigma
   A 130  SER  O
   A 130  SER  C
   A 131  ILE  N         123.00   116.28     6.72  1.60e+00  1.76e+01   4.2*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.75     5.45  1.30e+00  1.76e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.79     5.41  1.30e+00  1.73e+01   4.2*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   117.51    -7.01  1.70e+00  1.70e+01   4.1*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  CB        110.50   103.53     6.97  1.70e+00  1.68e+01   4.1*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00   122.47   -11.47  2.80e+00  1.68e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.53     4.07  1.00e+00  1.66e+01   4.1*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10   117.83    -7.73  1.90e+00  1.65e+01   4.1*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   128.94    -7.24  1.80e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   26.036 (Z= 10.961)
  Mean delta:    3.180 (Z=  1.638)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00    47.58   132.42  5.00e+00  7.01e+02  26.5*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   -68.72  -111.28  5.00e+00  4.95e+02  22.3*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    73.45   106.55  5.00e+00  4.54e+02  21.3*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    98.13    81.87  5.00e+00  2.68e+02  16.4*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   102.41    77.59  5.00e+00  2.41e+02  15.5*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00  -106.55   -73.45  5.00e+00  2.16e+02  14.7*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   110.81    69.19  5.00e+00  1.91e+02  13.8*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -113.35   -66.65  5.00e+00  1.78e+02  13.3*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   118.77    61.23  5.00e+00  1.50e+02  12.2*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   119.52    60.48  5.00e+00  1.46e+02  12.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -120.56   -59.44  5.00e+00  1.41e+02  11.9*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   131.55    48.45  5.00e+00  9.39e+01   9.7*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -137.04   -42.96  5.00e+00  7.38e+01   8.6*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   139.80    40.20  5.00e+00  6.46e+01   8.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   141.70    38.30  5.00e+00  5.87e+01   7.7*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -142.60   -37.40  5.00e+00  5.59e+01   7.5*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -142.61   -37.39  5.00e+00  5.59e+01   7.5*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   144.51    35.49  5.00e+00  5.04e+01   7.1*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   147.65    32.35  5.00e+00  4.19e+01   6.5*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -150.65   -29.35  5.00e+00  3.45e+01   5.9*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA          0.00    29.27   -29.27  5.00e+00  3.43e+01   5.9*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -151.07   -28.93  5.00e+00  3.35e+01   5.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -152.40   -27.60  5.00e+00  3.05e+01   5.5*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   153.10    26.90  5.00e+00  2.90e+01   5.4*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   153.92    26.08  5.00e+00  2.72e+01   5.2*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   156.93    23.07  5.00e+00  2.13e+01   4.6*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   158.79    21.21  5.00e+00  1.80e+01   4.2*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   159.02    20.98  5.00e+00  1.76e+01   4.2*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   159.54    20.46  5.00e+00  1.67e+01   4.1*sigma
   A  52  PRO  CA
   A  52  PRO  C
   A  53  LEU  N
   A  53  LEU  CA        180.00  -159.74   -20.26  5.00e+00  1.64e+01   4.1*sigma

  Min. delta:    0.006
  Max. delta:  132.425
  Mean delta:   20.823

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -3.08     5.61  2.00e-01  7.86e+02  28.0*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.04     5.55  2.00e-01  7.70e+02  27.8*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.68     5.19  2.00e-01  6.73e+02  26.0*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.50     5.15  2.00e-01  6.62e+02  25.7*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.62     5.06  2.00e-01  6.39e+02  25.3*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.34     4.89  2.00e-01  5.97e+02  24.4*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.28     4.79  2.00e-01  5.73e+02  23.9*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.23     4.66  2.00e-01  5.44e+02  23.3*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -1.28     3.79  2.00e-01  3.60e+02  19.0*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -1.01     3.52  2.00e-01  3.10e+02  17.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.67     3.11  2.00e-01  2.41e+02  15.5*sigma

  Min. delta:    0.001
  Max. delta:    5.609
  Mean delta:    1.196

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.062       0.102       78.10   5.1*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.050       0.092       50.12   4.6*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  ND1
   A  43  HIS  CD2
   A  43  HIS  CE1
   A  43  HIS  NE2           0.075       0.091       83.68   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.083
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 125  LYS  HA , Angle CB-CA-HA, observed: 95.686, delta from target: 13.314
   A 115  ALA  HA , Angle C-CA-HA, observed: 94.795, delta from target: 14.205
   A 130  SER  HA , Angle CB-CA-HA, observed: 123.359, delta from target: -14.359
   A 128  MET  HA , Angle N-CA-HA, observed: 125.438, delta from target: -15.438
   A  79  LYS  HA , Angle N-CA-HA, observed: 125.632, delta from target: -15.632
   A 126  VAL  HA , Angle N-CA-HA, observed: 94.035, delta from target: 15.965
   A 131  ILE  HA , Angle CB-CA-HA, observed: 125.128, delta from target: -16.128
   A 127  ARG  HA , Angle C-CA-HA, observed: 89.670, delta from target: 19.330
   A 123  GLU  HA , Angle N-CA-HA, observed: 130.182, delta from target: -20.182
   A 130  SER  HA , Angle C-CA-HA, observed: 87.696, delta from target: 21.304
   A 125  LYS  HA , Angle C-CA-HA, observed: 87.217, delta from target: 21.783
   A  51  ILE  HA , Angle C-CA-HA, observed: 83.609, delta from target: 25.391
   A  51  ILE  HA , Angle CB-CA-HA, observed: 82.642, delta from target: 26.358
   A 127  ARG  HA , Angle CB-CA-HA, observed: 137.384, delta from target: -28.384
   A 127  ARG  HA , Angle N-CA-HA, observed: 74.124, delta from target: 35.876

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.137   2242  Z= 0.642
    Angle     :  2.872  35.876   4079  Z= 1.227
    Chirality :  1.196   5.609    176
    Planarity :  0.013   0.078    327
    Dihedral  : 16.993 132.425    769
    Min Nonbonded Distance : 1.466
  
  Molprobity Statistics.
    All-atom Clashscore : 16.23
    Ramachandran Plot:
      Outliers :  9.49 %
      Allowed  :  8.03 %
      Favored  : 82.48 %
    Rotamer:
      Outliers : 10.48 %
      Allowed  :  2.42 %
      Favored  : 87.10 %
    Cbeta Deviations : 15.15 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 1.53 %
      Twisted Proline : 0.00 %
      Twisted General : 14.50 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.94 (0.57), residues: 137
    helix: -1.70 (0.51), residues: 63
    sheet:  None (None), residues: 0
    loop : -3.62 (0.59), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.024   0.006   HIS A  43 
   PHE   0.041   0.010   PHE A  67 
   TYR   0.137   0.024   TYR A  91 
   ARG   0.072   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.024   0.006   HIS A  43 
   PHE   0.019   0.008   PHE A  67 
   TYR   0.102   0.024   TYR A  91 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   61": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   70": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A LEU  119": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   5.84 %
                favored =  81.02 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    16
  Clashscore            =  17.58
  RMS(bonds)            =   0.0121
  RMS(angles)           =   2.79
  MolProbity score      =   3.12

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   5.11 %
                favored =  79.56 %
  Rotamer outliers      =   8.06 %
  C-beta deviations     =    14
  Clashscore            =   8.57
  RMS(bonds)            =   0.0111
  RMS(angles)           =   2.42
  MolProbity score      =   2.89

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Ramachandran outliers =   6.57 %
                favored =  87.59 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    15
  Clashscore            =  22.54
  RMS(bonds)            =   0.0117
  RMS(angles)           =   2.71
  MolProbity score      =   3.07

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   9.49 %
                favored =  82.48 %
  Rotamer outliers      =  10.48 %
  C-beta deviations     =    20
  Clashscore            =  16.23
  RMS(bonds)            =   0.0124
  RMS(angles)           =   2.87
  MolProbity score      =   3.19

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  89  TYR  C
   A  90  SER  N           1.33     1.21     0.12  1.40e-02  6.96e+01   8.3*sigma
   A  77  ILE  CA
   A  77  ILE  C           1.52     1.39     0.14  2.10e-02  4.40e+01   6.6*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.63    -0.11  1.80e-02  4.05e+01   6.4*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.57    -0.11  1.90e-02  3.45e+01   5.9*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.64    -0.12  2.10e-02  3.06e+01   5.5*sigma
   A  42  GLY  C
   A  43  HIS  N           1.33     1.27     0.06  1.40e-02  1.72e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.139 (Z=  8.342)
  Mean delta:    0.019 (Z=  1.006)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  CB        110.50    88.75    21.75  1.70e+00  1.64e+02  12.8*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   127.40   -16.90  1.50e+00  1.27e+02  11.3*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10    88.79    21.31  1.90e+00  1.26e+02  11.2*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50    92.99    18.51  1.70e+00  1.18e+02  10.9*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   102.47    19.23  1.80e+00  1.14e+02  10.7*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   105.96    17.04  1.60e+00  1.13e+02  10.7*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   128.05   -17.95  1.90e+00  8.93e+01   9.4*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   137.01   -26.01  2.80e+00  8.63e+01   9.3*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   137.39   -15.69  1.80e+00  7.59e+01   8.7*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  CB        111.50    97.22    14.28  1.70e+00  7.06e+01   8.4*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  C         111.00   133.13   -22.13  2.80e+00  6.24e+01   7.9*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    96.20    13.90  1.90e+00  5.36e+01   7.3*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   122.45   -12.05  1.70e+00  5.02e+01   7.1*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   102.35     9.65  1.40e+00  4.75e+01   6.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   102.82    13.38  2.00e+00  4.47e+01   6.7*sigma
   A  41  VAL  C
   A  42  GLY  N
   A  42  GLY  CA        121.70   109.99    11.71  1.80e+00  4.23e+01   6.5*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   133.38   -11.68  1.80e+00  4.21e+01   6.5*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    92.97    18.03  2.80e+00  4.15e+01   6.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   103.34    12.86  2.00e+00  4.14e+01   6.4*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   121.19   -10.79  1.70e+00  4.03e+01   6.3*sigma
   A  42  GLY  CA
   A  42  GLY  C
   A  43  HIS  N         116.20   103.50    12.70  2.00e+00  4.03e+01   6.3*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   110.56    11.14  1.80e+00  3.83e+01   6.2*sigma
   A  41  VAL  CA
   A  41  VAL  CB
   A  41  VAL  CG2       110.40   120.90   -10.50  1.70e+00  3.81e+01   6.2*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.66    -6.06  1.00e+00  3.67e+01   6.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  89  TYR  O         120.80   130.79    -9.99  1.70e+00  3.45e+01   5.9*sigma
   A  83  THR  CA
   A  83  THR  CB
   A  83  THR  CG2       110.50   120.32    -9.82  1.70e+00  3.34e+01   5.8*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   120.17    -9.67  1.70e+00  3.23e+01   5.7*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   113.92     9.08  1.60e+00  3.22e+01   5.7*sigma
   A  77  ILE  O
   A  77  ILE  C
   A  78  ILE  N         123.00   131.98    -8.98  1.60e+00  3.15e+01   5.6*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   131.74   -10.04  1.80e+00  3.11e+01   5.6*sigma
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        121.70   131.52    -9.82  1.80e+00  2.97e+01   5.5*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   126.13   -15.13  2.80e+00  2.92e+01   5.4*sigma
   A 139  HIS  C
   A 139  HIS  CA
   A 139  HIS  CB        110.10   120.23   -10.13  1.90e+00  2.84e+01   5.3*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80    99.14    11.66  2.20e+00  2.81e+01   5.3*sigma
   A  42  GLY  C
   A  43  HIS  N
   A  43  HIS  CA        121.70   131.11    -9.41  1.80e+00  2.73e+01   5.2*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   112.36     9.34  1.80e+00  2.69e+01   5.2*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   119.89    -9.79  1.90e+00  2.65e+01   5.2*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   126.44   -10.24  2.00e+00  2.62e+01   5.1*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   130.82    -9.12  1.80e+00  2.57e+01   5.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    97.01    13.99  2.80e+00  2.50e+01   5.0*sigma
   A  43  HIS  CA
   A  43  HIS  CB
   A  43  HIS  CG        113.80   118.76    -4.96  1.00e+00  2.46e+01   5.0*sigma
   A  82  THR  CA
   A  82  THR  CB
   A  82  THR  CG2       110.50   118.92    -8.42  1.70e+00  2.45e+01   5.0*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   118.74    -8.24  1.70e+00  2.35e+01   4.8*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   130.37    -8.67  1.80e+00  2.32e+01   4.8*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   130.17    -8.47  1.80e+00  2.22e+01   4.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   106.96     9.24  2.00e+00  2.13e+01   4.6*sigma
   A  52  PRO  C
   A  52  PRO  CA
   A  52  PRO  CB        110.10   118.87    -8.77  1.90e+00  2.13e+01   4.6*sigma
   A  82  THR  OG1
   A  82  THR  CB
   A  82  THR  CG2       109.30   100.12     9.18  2.00e+00  2.11e+01   4.6*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.28     5.92  1.30e+00  2.07e+01   4.6*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   118.72    -8.62  1.90e+00  2.06e+01   4.5*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50   103.87     7.63  1.70e+00  2.01e+01   4.5*sigma
   A 106  ALA  N
   A 106  ALA  CA
   A 106  ALA  CB        110.40   103.71     6.69  1.50e+00  1.99e+01   4.5*sigma
   A  86  ILE  C
   A  86  ILE  CA
   A  86  ILE  CB        111.60   120.50    -8.90  2.00e+00  1.98e+01   4.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O         120.80   128.22    -7.42  1.70e+00  1.90e+01   4.4*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   129.53    -7.83  1.80e+00  1.89e+01   4.4*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  C         111.00   123.09   -12.09  2.80e+00  1.86e+01   4.3*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   107.69     8.51  2.00e+00  1.81e+01   4.3*sigma
   A  88  ASP  O
   A  88  ASP  C
   A  89  TYR  N         123.00   116.23     6.77  1.60e+00  1.79e+01   4.2*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   107.75     8.45  2.00e+00  1.79e+01   4.2*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   103.32     7.18  1.70e+00  1.78e+01   4.2*sigma
   A  85  LYS  N
   A  85  LYS  CA
   A  85  LYS  CB        110.50   103.35     7.15  1.70e+00  1.77e+01   4.2*sigma
   A 117  PRO  N
   A 117  PRO  CA
   A 117  PRO  C         112.10   122.61   -10.51  2.50e+00  1.77e+01   4.2*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   129.26    -7.56  1.80e+00  1.76e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma
   A 114  PRO  N
   A 114  PRO  CA
   A 114  PRO  CB        103.00   107.56    -4.56  1.10e+00  1.72e+01   4.1*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   121.34    -7.44  1.80e+00  1.71e+01   4.1*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   129.13    -7.43  1.80e+00  1.70e+01   4.1*sigma
   A 124  ALA  O
   A 124  ALA  C
   A 125  LYS  N         123.00   116.43     6.57  1.60e+00  1.68e+01   4.1*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.55     4.05  1.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   26.011 (Z= 12.795)
  Mean delta:    3.446 (Z=  1.821)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    73.33   106.67  5.00e+00  4.55e+02  21.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   -73.61  -106.39  5.00e+00  4.53e+02  21.3*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -74.52  -105.48  5.00e+00  4.45e+02  21.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -81.76   -98.24  5.00e+00  3.86e+02  19.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    88.71    91.29  5.00e+00  3.33e+02  18.3*sigma
   A  41  VAL  CA
   A  41  VAL  C
   A  42  GLY  N
   A  42  GLY  CA        180.00   -89.24   -90.76  5.00e+00  3.29e+02  18.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   -91.67   -88.33  5.00e+00  3.12e+02  17.7*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   104.64    75.36  5.00e+00  2.27e+02  15.1*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   109.72    70.28  5.00e+00  1.98e+02  14.1*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00  -111.99   -68.01  5.00e+00  1.85e+02  13.6*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   114.74    65.26  5.00e+00  1.70e+02  13.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   120.00    60.00  5.00e+00  1.44e+02  12.0*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -120.66   -59.34  5.00e+00  1.41e+02  11.9*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   123.58    56.42  5.00e+00  1.27e+02  11.3*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   129.18    50.82  5.00e+00  1.03e+02  10.2*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   130.89    49.11  5.00e+00  9.65e+01   9.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   131.25    48.75  5.00e+00  9.50e+01   9.7*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   142.92    37.08  5.00e+00  5.50e+01   7.4*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   144.96    35.04  5.00e+00  4.91e+01   7.0*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   146.73    33.27  5.00e+00  4.43e+01   6.7*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00  -151.58   -28.42  5.00e+00  3.23e+01   5.7*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   154.04    25.96  5.00e+00  2.70e+01   5.2*sigma
   A 111  TYR  CA
   A 111  TYR  C
   A 112  VAL  N
   A 112  VAL  CA        180.00   154.25    25.75  5.00e+00  2.65e+01   5.1*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   154.98    25.02  5.00e+00  2.50e+01   5.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -157.68   -22.32  5.00e+00  1.99e+01   4.5*sigma
   A  52  PRO  CA
   A  52  PRO  C
   A  53  LEU  N
   A  53  LEU  CA        180.00   158.54    21.46  5.00e+00  1.84e+01   4.3*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -159.22   -20.78  5.00e+00  1.73e+01   4.2*sigma
   A 102  PRO  CA
   A 102  PRO  C
   A 103  ASP  N
   A 103  ASP  CA        180.00  -159.26   -20.74  5.00e+00  1.72e+01   4.1*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00  -159.34   -20.66  5.00e+00  1.71e+01   4.1*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -159.44   -20.56  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.047
  Max. delta:  106.672
  Mean delta:   21.391

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.31     5.82  2.00e-01  8.47e+02  29.1*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -3.03     5.48  2.00e-01  7.50e+02  27.4*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.79     5.23  2.00e-01  6.83e+02  26.1*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.60     5.11  2.00e-01  6.52e+02  25.5*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.50     5.01  2.00e-01  6.27e+02  25.0*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.47     4.98  2.00e-01  6.19e+02  24.9*sigma
   A 138  HIS  CA
   A 138  HIS  N
   A 138  HIS  C
   A 138  HIS  CB          2.51    -2.38     4.89  2.00e-01  5.98e+02  24.4*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  C
   A  52  PRO  CB          2.72    -2.15     4.87  2.00e-01  5.92e+02  24.3*sigma
   A 130  SER  CA
   A 130  SER  N
   A 130  SER  C
   A 130  SER  CB          2.51    -2.14     4.65  2.00e-01  5.41e+02  23.2*sigma
   A  83  THR  CA
   A  83  THR  N
   A  83  THR  C
   A  83  THR  CB          2.53    -2.05     4.58  2.00e-01  5.24e+02  22.9*sigma
   A 129  ARG  CA
   A 129  ARG  N
   A 129  ARG  C
   A 129  ARG  CB          2.51    -1.99     4.50  2.00e-01  5.06e+02  22.5*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51    -1.24     3.75  2.00e-01  3.52e+02  18.8*sigma
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51    -0.90     3.41  2.00e-01  2.90e+02  17.0*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51     1.30     1.21  2.00e-01  3.68e+01   6.1*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51     1.40     1.11  2.00e-01  3.07e+01   5.5*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48     1.48     1.00  2.00e-01  2.52e+01   5.0*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.64     0.87  2.00e-01  1.90e+01   4.4*sigma
   A 131  ILE  CA
   A 131  ILE  N
   A 131  ILE  C
   A 131  ILE  CB          2.43     1.59     0.85  2.00e-01  1.79e+01   4.2*sigma

  Min. delta:    0.002
  Max. delta:    5.822
  Mean delta:    1.335

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O
   A 127  ARG  N             0.087       0.151       76.52   7.6*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O
   A  91  TYR  N             0.075       0.129       56.06   6.5*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.065       0.123       85.02   6.1*sigma
   A  83  THR  CA
   A  83  THR  C
   A  83  THR  O
   A  84  GLU  N             0.047       0.082       22.37   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.106
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 128  MET  HA , Angle CB-CA-HA, observed: 96.382, delta from target: 12.618
   A  90  SER  HA , Angle CB-CA-HA, observed: 96.141, delta from target: 12.859
   A  74  ASP  HA , Angle CB-CA-HA, observed: 95.689, delta from target: 13.311
   A  90  SER  HA , Angle N-CA-HA, observed: 96.620, delta from target: 13.380
   A  82  THR  HB , Angle CA-CB-HB, observed: 95.411, delta from target: 13.589
   A  83  THR  HB , Angle CA-CB-HB, observed: 95.383, delta from target: 13.617
   A 126  VAL  HA , Angle N-CA-HA, observed: 123.771, delta from target: -13.771
   A 126  VAL  HB , Angle CA-CB-HB, observed: 94.946, delta from target: 14.054
   A  83  THR  HA , Angle C-CA-HA, observed: 94.738, delta from target: 14.262
   A  81  TYR  HA , Angle C-CA-HA, observed: 93.832, delta from target: 15.168
   A  52  PRO  HA , Angle C-CA-HA, observed: 92.768, delta from target: 16.232
   A  79  LYS  HA , Angle C-CA-HA, observed: 125.525, delta from target: -16.525
   A 131  ILE  HA , Angle C-CA-HA, observed: 92.279, delta from target: 16.721
   A 139  HIS  HA , Angle C-CA-HA, observed: 92.122, delta from target: 16.878
   A 128  MET  HA , Angle N-CA-HA, observed: 129.908, delta from target: -19.908
   A  77  ILE  HB , Angle CA-CB-HB, observed: 88.560, delta from target: 20.440
   A 124  ALA  HA , Angle CB-CA-HA, observed: 87.610, delta from target: 21.390
   A 127  ARG  HA , Angle C-CA-HA, observed: 86.781, delta from target: 22.219
   A  88  ASP  HA , Angle C-CA-HA, observed: 84.527, delta from target: 24.473
   A  88  ASP  HA , Angle CB-CA-HA, observed: 133.536, delta from target: -24.536
   A  91  TYR  HA , Angle C-CA-HA, observed: 84.375, delta from target: 24.625
   A  88  ASP  HA , Angle N-CA-HA, observed: 76.557, delta from target: 33.443
   A  89  TYR  HA , Angle CB-CA-HA, observed: 144.936, delta from target: -35.936

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.014   0.139   2242  Z= 0.717
    Angle     :  3.043  35.936   4079  Z= 1.335
    Chirality :  1.335   5.822    176
    Planarity :  0.015   0.106    327
    Dihedral  : 17.554 106.672    769
    Min Nonbonded Distance : 1.543
  
  Molprobity Statistics.
    All-atom Clashscore : 22.99
    Ramachandran Plot:
      Outliers : 12.41 %
      Allowed  : 14.60 %
      Favored  : 72.99 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  4.03 %
      Favored  : 90.32 %
    Cbeta Deviations : 20.45 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 15.27 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.02 (0.66), residues: 137
    helix: -1.66 (0.54), residues: 62
    sheet:  None (None), residues: 0
    loop : -3.75 (0.73), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.005   HIS A  43 
   PHE   0.042   0.010   PHE A  45 
   TYR   0.150   0.021   TYR A  50 
   ARG   0.020   0.005   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.005   HIS A  43 
   PHE   0.023   0.008   PHE A  67 
   TYR   0.123   0.022   TYR A  50 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =  12.41 %
                favored =  72.99 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =    27
  Clashscore            =  22.99
  RMS(bonds)            =   0.0138
  RMS(angles)           =   3.04
  MolProbity score      =   3.24

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.499)
  Mean delta:    0.013 (Z=  0.652)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   133.33   -11.63  1.80e+00  4.17e+01   6.5*sigma
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        121.70   132.35   -10.65  1.80e+00  3.50e+01   5.9*sigma
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        121.70   129.51    -7.81  1.80e+00  1.88e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.39     4.21  1.00e+00  1.77e+01   4.2*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  83  THR  CA
   A  83  THR  CB
   A  83  THR  CG2       110.50   117.51    -7.01  1.70e+00  1.70e+01   4.1*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  CD2       131.20   125.93     5.27  1.30e+00  1.64e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   11.626 (Z=  6.459)
  Mean delta:    1.919 (Z=  1.062)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   -84.83   -95.17  5.00e+00  3.62e+02  19.0*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   157.96    22.04  5.00e+00  1.94e+01   4.4*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   158.12    21.88  5.00e+00  1.91e+01   4.4*sigma

  Min. delta:    0.075
  Max. delta:   95.170
  Mean delta:   17.816

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  CA
   A  83  THR  N
   A  83  THR  C
   A  83  THR  CB          2.53    -1.82     4.34  2.00e-01  4.71e+02  21.7*sigma

  Min. delta:    0.000
  Max. delta:    4.341
  Mean delta:    0.342

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.110       0.202      243.37  10.1*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  ND1
   A 138  HIS  CD2
   A 138  HIS  CE1
   A 138  HIS  NE2           0.063       0.083       58.82   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.110
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.464
    Angle     :  1.763  11.626   4079  Z= 0.785
    Chirality :  0.342   4.341    176
    Planarity :  0.013   0.104    327
    Dihedral  : 14.339  95.170    769
    Min Nonbonded Distance : 1.734
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  6.57 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  1.61 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.34 (0.59), residues: 137
    helix: -0.64 (0.51), residues: 82
    sheet:  None (None), residues: 0
    loop : -2.98 (0.58), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.031   0.009   HIS A 139 
   PHE   0.058   0.012   PHE A  45 
   TYR   0.250   0.026   TYR A 111 
   ARG   0.053   0.013   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.031   0.009   HIS A 139 
   PHE   0.026   0.008   PHE A  45 
   TYR   0.202   0.028   TYR A 111 
   ARG   0.008   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN
   A 139  HIS

=================================== Summary ===================================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 128  MET  N
   A 128  MET  CA          1.46     1.82    -0.37  1.90e-02  3.70e+02  19.2*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.69    -0.23  1.90e-02  1.50e+02  12.3*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.75    -0.22  2.10e-02  1.14e+02  10.7*sigma
   A 132  LEU  N
   A 132  LEU  CA          1.46     1.66    -0.20  1.90e-02  1.11e+02  10.5*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.65    -0.19  1.90e-02  1.03e+02  10.1*sigma
   A 131  ILE  N
   A 131  ILE  CA          1.46     1.62    -0.17  1.90e-02  7.58e+01   8.7*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.45    -0.12  1.40e-02  7.33e+01   8.6*sigma
   A 133  GLU  N
   A 133  GLU  CA          1.46     1.61    -0.16  1.90e-02  6.70e+01   8.2*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.61    -0.15  1.90e-02  6.27e+01   7.9*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.65    -0.14  1.80e-02  5.83e+01   7.6*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.60    -0.14  1.90e-02  5.68e+01   7.5*sigma
   A  78  ILE  N
   A  78  ILE  CA          1.46     1.60    -0.14  1.90e-02  5.57e+01   7.5*sigma
   A 131  ILE  CA
   A 131  ILE  C           1.52     1.68    -0.15  2.10e-02  5.11e+01   7.2*sigma
   A  77  ILE  N
   A  77  ILE  CA          1.46     1.59    -0.13  1.90e-02  4.75e+01   6.9*sigma
   A 128  MET  CA
   A 128  MET  C           1.52     1.38     0.14  2.10e-02  4.55e+01   6.7*sigma
   A 130  SER  CA
   A 130  SER  C           1.52     1.66    -0.14  2.10e-02  4.39e+01   6.6*sigma
   A  78  ILE  CB
   A  78  ILE  CG1         1.53     1.65    -0.12  2.00e-02  3.89e+01   6.2*sigma
   A  89  TYR  N
   A  89  TYR  CA          1.46     1.58    -0.12  1.90e-02  3.80e+01   6.2*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.55    -0.10  1.60e-02  3.63e+01   6.0*sigma
   A  78  ILE  CG1
   A  78  ILE  CD1         1.51     1.75    -0.23  3.90e-02  3.62e+01   6.0*sigma
   A  88  ASP  C
   A  89  TYR  N           1.33     1.41    -0.08  1.40e-02  3.38e+01   5.8*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.64    -0.11  2.10e-02  2.97e+01   5.4*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.36     0.10  1.90e-02  2.88e+01   5.4*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.64    -0.11  2.10e-02  2.79e+01   5.3*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.40    -0.07  1.40e-02  2.66e+01   5.2*sigma
   A 131  ILE  C
   A 132  LEU  N           1.33     1.40    -0.07  1.40e-02  2.55e+01   5.0*sigma
   A 122  ILE  C
   A 123  GLU  N           1.33     1.40    -0.07  1.40e-02  2.28e+01   4.8*sigma
   A  77  ILE  CA
   A  77  ILE  C           1.52     1.62    -0.10  2.10e-02  2.26e+01   4.8*sigma
   A  77  ILE  C
   A  78  ILE  N           1.33     1.39    -0.06  1.40e-02  2.08e+01   4.6*sigma
   A  76  SER  CA
   A  76  SER  C           1.52     1.62    -0.09  2.10e-02  1.93e+01   4.4*sigma
   A 134  HIS  N
   A 134  HIS  CA          1.46     1.54    -0.08  1.90e-02  1.71e+01   4.1*sigma
   A 114  PRO  C
   A 115  ALA  N           1.33     1.27     0.06  1.40e-02  1.68e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.366 (Z= 19.245)
  Mean delta:    0.030 (Z=  1.557)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   159.17   -37.47  1.80e+00  4.33e+02  20.8*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40    80.69    29.71  1.70e+00  3.05e+02  17.5*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50    83.41    27.09  1.70e+00  2.54e+02  15.9*sigma
   A  78  ILE  CG1
   A  78  ILE  CB
   A  78  ILE  CG2       110.70   156.22   -45.52  3.00e+00  2.30e+02  15.2*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   144.62   -22.92  1.80e+00  1.62e+02  12.7*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20    92.16    24.04  2.00e+00  1.44e+02  12.0*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   134.72   -25.62  2.20e+00  1.36e+02  11.6*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   140.83   -29.83  2.80e+00  1.14e+02  10.7*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   140.79   -19.09  1.80e+00  1.12e+02  10.6*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   123.02   -10.42  1.00e+00  1.09e+02  10.4*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   140.31   -18.61  1.80e+00  1.07e+02  10.3*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60    91.33    20.27  2.00e+00  1.03e+02  10.1*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00   138.94   -27.94  2.80e+00  9.95e+01  10.0*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    83.60    27.40  2.80e+00  9.58e+01   9.8*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    95.07    16.43  1.70e+00  9.34e+01   9.7*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   105.32    16.38  1.80e+00  8.29e+01   9.1*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   137.72   -16.02  1.80e+00  7.92e+01   8.9*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50    96.82    14.68  1.70e+00  7.45e+01   8.6*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20    99.01    17.19  2.00e+00  7.39e+01   8.6*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   126.04   -15.94  1.90e+00  7.04e+01   8.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   135.87   -14.17  1.80e+00  6.20e+01   7.9*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00   132.01   -21.01  2.80e+00  5.63e+01   7.5*sigma
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        121.70   135.16   -13.46  1.80e+00  5.59e+01   7.5*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   135.02   -13.32  1.80e+00  5.48e+01   7.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.00   -11.10  1.50e+00  5.47e+01   7.4*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   133.19   -12.39  1.70e+00  5.31e+01   7.3*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   134.75   -13.05  1.80e+00  5.26e+01   7.3*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   134.59   -12.89  1.80e+00  5.13e+01   7.2*sigma
   A 114  PRO  N
   A 114  PRO  CA
   A 114  PRO  C         112.10   129.85   -17.75  2.50e+00  5.04e+01   7.1*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   119.53    -6.93  1.00e+00  4.80e+01   6.9*sigma
   A  76  SER  N
   A  76  SER  CA
   A  76  SER  CB        110.50    98.81    11.69  1.70e+00  4.73e+01   6.9*sigma
   A  78  ILE  CB
   A  78  ILE  CG1
   A  78  ILE  CD1       113.80   128.02   -14.22  2.10e+00  4.59e+01   6.8*sigma
   A 132  LEU  N
   A 132  LEU  CA
   A 132  LEU  C         111.00   129.87   -18.87  2.80e+00  4.54e+01   6.7*sigma
   A 124  ALA  O
   A 124  ALA  C
   A 125  LYS  N         123.00   112.27    10.73  1.60e+00  4.50e+01   6.7*sigma
   A 126  VAL  O
   A 126  VAL  C
   A 127  ARG  N         123.00   133.72   -10.72  1.60e+00  4.49e+01   6.7*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   133.75   -12.05  1.80e+00  4.48e+01   6.7*sigma
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        121.70   109.70    12.00  1.80e+00  4.44e+01   6.7*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  C         111.00   129.34   -18.34  2.80e+00  4.29e+01   6.5*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40   100.64     9.76  1.50e+00  4.23e+01   6.5*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   122.31   -12.21  1.90e+00  4.13e+01   6.4*sigma
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        121.70   110.21    11.49  1.80e+00  4.07e+01   6.4*sigma
   A  76  SER  O
   A  76  SER  C
   A  77  ILE  N         123.00   112.96    10.04  1.60e+00  3.94e+01   6.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.67   -10.97  1.80e+00  3.71e+01   6.1*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   118.56    -5.96  1.00e+00  3.56e+01   6.0*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   120.38    -9.88  1.70e+00  3.38e+01   5.8*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   127.04   -16.04  2.80e+00  3.28e+01   5.7*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   124.12   -10.22  1.80e+00  3.23e+01   5.7*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    95.31    15.69  2.80e+00  3.14e+01   5.6*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O         120.80   130.19    -9.39  1.70e+00  3.05e+01   5.5*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   114.19     8.81  1.60e+00  3.03e+01   5.5*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   121.67   -10.27  1.90e+00  2.92e+01   5.4*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  C         111.00   126.04   -15.04  2.80e+00  2.88e+01   5.4*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   112.13     9.57  1.80e+00  2.83e+01   5.3*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   131.19    -9.49  1.80e+00  2.78e+01   5.3*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.33     5.27  1.00e+00  2.77e+01   5.3*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   124.79    -7.89  1.50e+00  2.76e+01   5.3*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   120.00    -9.90  1.90e+00  2.72e+01   5.2*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.75    -5.15  1.00e+00  2.65e+01   5.1*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   123.05    -9.15  1.80e+00  2.58e+01   5.1*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N         116.20   106.06    10.14  2.00e+00  2.57e+01   5.1*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   130.78    -9.08  1.80e+00  2.54e+01   5.0*sigma
   A 110  ASP  CA
   A 110  ASP  CB
   A 110  ASP  CG        112.60   117.59    -4.99  1.00e+00  2.49e+01   5.0*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   126.03    -9.83  2.00e+00  2.41e+01   4.9*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   119.42    -9.32  1.90e+00  2.41e+01   4.9*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.39    -9.79  2.00e+00  2.40e+01   4.9*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N         116.20   125.90    -9.70  2.00e+00  2.35e+01   4.9*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   115.54     7.46  1.60e+00  2.17e+01   4.7*sigma
   A 119  LEU  N
   A 119  LEU  CA
   A 119  LEU  C         111.00   123.99   -12.99  2.80e+00  2.15e+01   4.6*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   125.39    -9.19  2.00e+00  2.11e+01   4.6*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N         116.20   107.08     9.12  2.00e+00  2.08e+01   4.6*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  C         111.00    98.23    12.77  2.80e+00  2.08e+01   4.6*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   120.56    -8.96  2.00e+00  2.01e+01   4.5*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   103.15     7.35  1.70e+00  1.87e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.36     4.24  1.00e+00  1.80e+01   4.2*sigma
   A  95  ASP  C
   A  95  ASP  CA
   A  95  ASP  CB        110.10   118.05    -7.95  1.90e+00  1.75e+01   4.2*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   129.17    -7.47  1.80e+00  1.72e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.45     4.15  1.00e+00  1.72e+01   4.1*sigma
   A  39  LEU  N
   A  39  LEU  CA
   A  39  LEU  CB        110.50   103.45     7.05  1.70e+00  1.72e+01   4.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   124.46    -8.26  2.00e+00  1.70e+01   4.1*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.96     5.24  1.30e+00  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   45.522 (Z= 20.819)
  Mean delta:    4.288 (Z=  2.183)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00    61.47   118.53  5.00e+00  5.62e+02  23.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   -66.01  -113.99  5.00e+00  5.20e+02  22.8*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -79.64  -100.36  5.00e+00  4.03e+02  20.1*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   -92.07   -87.93  5.00e+00  3.09e+02  17.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    94.53    85.47  5.00e+00  2.92e+02  17.1*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   101.24    78.76  5.00e+00  2.48e+02  15.8*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -101.81   -78.19  5.00e+00  2.45e+02  15.6*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   108.84    71.16  5.00e+00  2.03e+02  14.2*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   109.93    70.07  5.00e+00  1.96e+02  14.0*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -114.46   -65.54  5.00e+00  1.72e+02  13.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -115.58   -64.42  5.00e+00  1.66e+02  12.9*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -120.56   -59.44  5.00e+00  1.41e+02  11.9*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   126.09    53.91  5.00e+00  1.16e+02  10.8*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   126.72    53.28  5.00e+00  1.14e+02  10.7*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   127.61    52.39  5.00e+00  1.10e+02  10.5*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -127.83   -52.17  5.00e+00  1.09e+02  10.4*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -129.24   -50.76  5.00e+00  1.03e+02  10.2*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   137.09    42.91  5.00e+00  7.37e+01   8.6*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   140.61    39.39  5.00e+00  6.21e+01   7.9*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   140.81    39.19  5.00e+00  6.14e+01   7.8*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   141.45    38.55  5.00e+00  5.94e+01   7.7*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   144.21    35.79  5.00e+00  5.12e+01   7.2*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   150.94    29.06  5.00e+00  3.38e+01   5.8*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   151.23    28.77  5.00e+00  3.31e+01   5.8*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -151.74   -28.26  5.00e+00  3.19e+01   5.7*sigma
   A  70  LEU  CA
   A  70  LEU  C
   A  71  ILE  N
   A  71  ILE  CA        180.00   151.86    28.14  5.00e+00  3.17e+01   5.6*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -154.19   -25.81  5.00e+00  2.67e+01   5.2*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00  -157.14   -22.86  5.00e+00  2.09e+01   4.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   157.79    22.21  5.00e+00  1.97e+01   4.4*sigma
   A  38  ILE  CA
   A  38  ILE  C
   A  39  LEU  N
   A  39  LEU  CA        180.00   157.89    22.11  5.00e+00  1.95e+01   4.4*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA          0.00   -21.73    21.73  5.00e+00  1.89e+01   4.3*sigma

  Min. delta:    0.008
  Max. delta:  118.529
  Mean delta:   21.885

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -3.11     5.59  2.00e-01  7.82e+02  28.0*sigma
   A 131  ILE  CA
   A 131  ILE  N
   A 131  ILE  C
   A 131  ILE  CB          2.43    -2.93     5.36  2.00e-01  7.19e+02  26.8*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.65     5.16  2.00e-01  6.66e+02  25.8*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.45     5.09  2.00e-01  6.48e+02  25.5*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.40     5.05  2.00e-01  6.36e+02  25.2*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.55     4.99  2.00e-01  6.22e+02  24.9*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.43     4.98  2.00e-01  6.20e+02  24.9*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.46     4.97  2.00e-01  6.17e+02  24.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.33     4.77  2.00e-01  5.68e+02  23.8*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -1.90     4.41  2.00e-01  4.87e+02  22.1*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -1.18     3.82  2.00e-01  3.66e+02  19.1*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -1.16     3.68  2.00e-01  3.39e+02  18.4*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.08     3.51  2.00e-01  3.08e+02  17.6*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -0.72     3.15  2.00e-01  2.49e+02  15.8*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     1.24     1.27  2.00e-01  4.01e+01   6.3*sigma
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51     1.68     0.83  2.00e-01  1.71e+01   4.1*sigma

  Min. delta:    0.001
  Max. delta:    5.595
  Mean delta:    1.335

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.089       0.175      158.91   8.7*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.070       0.124       97.71   6.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O
   A  80  GLY  N             0.069       0.120       47.99   6.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 128  MET  O
   A 129  ARG  N             0.054       0.094       29.30   4.7*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O
   A 124  ALA  N             0.053       0.092       28.21   4.6*sigma
   A  97  SER  CA
   A  97  SER  C
   A  97  SER  O
   A  98  SER  N             0.050       0.086       24.90   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.089
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="ARG A 127  conformer  : H 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 127  ARG  HA , Angle C-CA-HA, observed: 96.990, delta from target: 12.010
   A  81  TYR  HA , Angle CB-CA-HA, observed: 121.268, delta from target: -12.268
   A 124  ALA  HA , Angle N-CA-HA, observed: 122.426, delta from target: -12.426
   A 119  LEU  HA , Angle CB-CA-HA, observed: 121.467, delta from target: -12.467
   A  89  TYR  HA , Angle N-CA-HA, observed: 96.916, delta from target: 13.084
   A 132  LEU  HA , Angle CB-CA-HA, observed: 122.109, delta from target: -13.109
   A 133  GLU  HA , Angle N-CA-HA, observed: 96.637, delta from target: 13.363
   A 116  ASP  HA , Angle N-CA-HA, observed: 96.257, delta from target: 13.743
   A  79  LYS  HA , Angle N-CA-HA, observed: 123.901, delta from target: -13.901
   A 130  SER  HA , Angle CB-CA-HA, observed: 123.336, delta from target: -14.336
   A  51  ILE  HA , Angle CB-CA-HA, observed: 94.390, delta from target: 14.610
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.507, delta from target: 16.493
   A 122  ILE  HA , Angle C-CA-HA, observed: 92.374, delta from target: 16.626
   A 114  PRO  HA , Angle CB-CA-HA, observed: 126.588, delta from target: -17.588
   A  79  LYS  H  , Angle CA-N-H, observed: 96.383, delta from target: 17.617
   A 131  ILE  HA , Angle C-CA-HA, observed: 91.352, delta from target: 17.648
   A 132  LEU  HA , Angle N-CA-HA, observed: 92.325, delta from target: 17.675
   A  79  LYS  HA , Angle CB-CA-HA, observed: 91.259, delta from target: 17.741
   A  81  TYR  HA , Angle N-CA-HA, observed: 92.058, delta from target: 17.942
   A 128  MET  HA , Angle N-CA-HA, observed: 129.476, delta from target: -19.476
   A  79  LYS  H  , Angle C-N-H, observed: 104.443, delta from target: 19.857
   A 132  LEU  HA , Angle C-CA-HA, observed: 89.107, delta from target: 19.893
   A 122  ILE  HA , Angle CB-CA-HA, observed: 129.985, delta from target: -20.985
   A  88  ASP  HA , Angle N-CA-HA, observed: 88.568, delta from target: 21.432
   A  92  THR  HA , Angle C-CA-HA, observed: 87.446, delta from target: 21.554
   A  92  THR  HA , Angle N-CA-HA, observed: 132.046, delta from target: -22.046
   A  81  TYR  HA , Angle C-CA-HA, observed: 85.439, delta from target: 23.561
   A  78  ILE  HA , Angle N-CA-HA, observed: 86.221, delta from target: 23.779
   A  77  ILE  HA , Angle N-CA-HA, observed: 82.389, delta from target: 27.611
   A  92  THR  HA , Angle CB-CA-HA, observed: 80.825, delta from target: 28.175
   A  78  ILE  HA , Angle CB-CA-HA, observed: 139.257, delta from target: -30.257
   A  77  ILE  HA , Angle C-CA-HA, observed: 69.840, delta from target: 39.160
   A  77  ILE  HA , Angle CB-CA-HA, observed: 149.053, delta from target: -40.053
   A  78  ILE  HB , Angle CA-CB-HB, observed: 166.531, delta from target: -57.531

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.021   0.366   2241  Z= 1.108
    Angle     :  3.754  57.531   4077  Z= 1.611
    Chirality :  1.335   5.595    176
    Planarity :  0.014   0.091    326
    Dihedral  : 17.553 118.529    769
    Min Nonbonded Distance : 1.378
  
  Molprobity Statistics.
    All-atom Clashscore : 40.14
    Ramachandran Plot:
      Outliers : 16.79 %
      Allowed  :  8.76 %
      Favored  : 74.45 %
    Rotamer:
      Outliers : 11.29 %
      Allowed  :  7.26 %
      Favored  : 81.45 %
    Cbeta Deviations : 16.67 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 1.53 %
      Twisted Proline : 0.00 %
      Twisted General : 16.79 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.20 (0.62), residues: 137
    helix: -2.64 (0.50), residues: 72
    sheet:  None (None), residues: 0
    loop : -2.93 (0.74), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.098   0.025   PHE A  15 
   TYR   0.235   0.029   TYR A  91 
   ARG   0.026   0.006   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.070   0.027   PHE A  15 
   TYR   0.175   0.033   TYR A  91 
   ARG   0.002   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Time building chain proxies: 0.98, per 1000 atoms: 0.44
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.581, 48.485, 50.625, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   0.73 %
                favored =  92.70 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     1
  Clashscore            =   1.35
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.76
  MolProbity score      =   1.71

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.954, 63.27, 59.634, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

  Ramachandran outliers =  16.79 %
                favored =  74.45 %
  Rotamer outliers      =  11.29 %
  C-beta deviations     =    22
  Clashscore            =  40.14
  RMS(bonds)            =   0.0214
  RMS(angles)           =   3.75
  MolProbity score      =   3.68

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Time building chain proxies: 0.80, per 1000 atoms: 0.36
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (43.985, 45.278, 50.597, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.072 (Z=  3.575)
  Mean delta:    0.014 (Z=  0.725)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   106.22    15.48  1.80e+00  7.40e+01   8.6*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    95.43    14.67  1.90e+00  5.96e+01   7.7*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    97.46    13.04  1.70e+00  5.88e+01   7.7*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   126.87   -15.27  2.00e+00  5.83e+01   7.6*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   135.37   -13.67  1.80e+00  5.77e+01   7.6*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.09   -11.19  1.50e+00  5.56e+01   7.5*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   108.76    12.94  1.80e+00  5.17e+01   7.2*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   118.92    -6.32  1.00e+00  4.00e+01   6.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.51   -10.81  1.80e+00  3.61e+01   6.0*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   131.32    -9.62  1.80e+00  2.86e+01   5.3*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   119.10    -8.70  1.70e+00  2.62e+01   5.1*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.71    -5.11  1.00e+00  2.61e+01   5.1*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.64   -10.04  2.00e+00  2.52e+01   5.0*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.32     5.88  1.30e+00  2.05e+01   4.5*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   118.46    -8.36  1.90e+00  1.93e+01   4.4*sigma
   A  82  THR  N
   A  82  THR  CA
   A  82  THR  CB        111.50   118.95    -7.45  1.70e+00  1.92e+01   4.4*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.57     5.63  1.30e+00  1.88e+01   4.3*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.45    -6.05  1.40e+00  1.87e+01   4.3*sigma
   A  82  THR  N
   A  82  THR  CA
   A  82  THR  C         111.00   122.79   -11.79  2.80e+00  1.77e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:   15.484 (Z=  8.602)
  Mean delta:    2.385 (Z=  1.307)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   -68.89  -111.11  5.00e+00  4.94e+02  22.2*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   -85.12   -94.88  5.00e+00  3.60e+02  19.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -87.65   -92.35  5.00e+00  3.41e+02  18.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -113.17   -66.83  5.00e+00  1.79e+02  13.4*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   133.72    46.28  5.00e+00  8.57e+01   9.3*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   133.80    46.20  5.00e+00  8.54e+01   9.2*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00  -139.92   -40.08  5.00e+00  6.43e+01   8.0*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   140.92    39.08  5.00e+00  6.11e+01   7.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA          0.00   -35.95    35.95  5.00e+00  5.17e+01   7.2*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -144.17   -35.83  5.00e+00  5.13e+01   7.2*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -152.54   -27.46  5.00e+00  3.02e+01   5.5*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   157.11    22.89  5.00e+00  2.10e+01   4.6*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA          0.00    22.40   -22.40  5.00e+00  2.01e+01   4.5*sigma

  Min. delta:    0.005
  Max. delta:  111.110
  Mean delta:   18.115

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.43     5.94  2.00e-01  8.83e+02  29.7*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.33     4.84  2.00e-01  5.87e+02  24.2*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -1.50     4.14  2.00e-01  4.29e+02  20.7*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.12     3.55  2.00e-01  3.15e+02  17.7*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -0.57     3.01  2.00e-01  2.26e+02  15.0*sigma
   A  82  THR  CA
   A  82  THR  N
   A  82  THR  C
   A  82  THR  CB          2.53     1.44     1.08  2.00e-01  2.93e+01   5.4*sigma

  Min. delta:    0.000
  Max. delta:    5.942
  Mean delta:    0.764

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.229       0.389     1049.71  19.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O
   A  91  TYR  N             0.052       0.090       27.35   4.5*sigma

  Min. delta:    0.000
  Max. delta:    0.229
  Mean delta:    0.021

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  78  ILE  HB , Angle CG1-CB-HB, observed: 96.559, delta from target: 12.441
   A  78  ILE  HA , Angle N-CA-HA, observed: 122.824, delta from target: -12.824
   A  79  LYS  HA , Angle CB-CA-HA, observed: 124.022, delta from target: -15.022
   A  51  ILE  HA , Angle CB-CA-HA, observed: 93.556, delta from target: 15.444
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.253, delta from target: 15.747
   A  82  THR  HA , Angle N-CA-HA, observed: 87.113, delta from target: 22.887
   A  78  ILE  HA , Angle C-CA-HA, observed: 63.035, delta from target: 45.965

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.072   2242  Z= 0.516
    Angle     :  2.280  45.965   4079  Z= 0.992
    Chirality :  0.764   5.942    176
    Planarity :  0.017   0.229    327
    Dihedral  : 14.715 111.110    769
    Min Nonbonded Distance : 1.499
  
  Molprobity Statistics.
    All-atom Clashscore : 13.98
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  7.30 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  3.23 %
      Favored  : 90.32 %
    Cbeta Deviations :  6.06 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 7.63 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.36 (0.62), residues: 137
    helix: -1.54 (0.48), residues: 85
    sheet:  None (None), residues: 0
    loop : -1.31 (0.81), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.107   0.021   PHE A  67 
   TYR   0.501   0.039   TYR A  91 
   ARG   0.033   0.007   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.076   0.023   PHE A  67 
   TYR   0.389   0.043   TYR A  91 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.64    -0.12  1.80e-02  4.74e+01   6.9*sigma
   A 123  GLU  C
   A 124  ALA  N           1.33     1.24     0.09  1.40e-02  3.87e+01   6.2*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.63    -0.11  2.10e-02  2.66e+01   5.2*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.55    -0.09  1.90e-02  2.14e+01   4.6*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.54    -0.08  1.90e-02  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.124 (Z=  6.882)
  Mean delta:    0.017 (Z=  0.910)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   135.22   -21.32  1.80e+00  1.40e+02  11.8*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   123.85   -13.35  1.50e+00  7.92e+01   8.9*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   124.89   -14.39  1.70e+00  7.17e+01   8.5*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   136.49   -14.79  1.80e+00  6.76e+01   8.2*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   125.51   -15.41  1.90e+00  6.58e+01   8.1*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   108.04    13.66  1.80e+00  5.76e+01   7.6*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   108.67    13.03  1.80e+00  5.24e+01   7.2*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  C         111.00    90.79    20.21  2.80e+00  5.21e+01   7.2*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   133.83   -12.13  1.80e+00  4.54e+01   6.7*sigma
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        121.70   133.80   -12.10  1.80e+00  4.52e+01   6.7*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   121.04   -10.64  1.70e+00  3.92e+01   6.3*sigma
   A 114  PRO  N
   A 114  PRO  CA
   A 114  PRO  CB        103.00   109.50    -6.50  1.10e+00  3.49e+01   5.9*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   120.49    -9.99  1.70e+00  3.45e+01   5.9*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   121.14   -11.04  1.90e+00  3.37e+01   5.8*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   120.33    -9.83  1.70e+00  3.34e+01   5.8*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50   101.72     9.78  1.70e+00  3.31e+01   5.8*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   132.05   -10.35  1.80e+00  3.31e+01   5.8*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   104.05     7.95  1.40e+00  3.22e+01   5.7*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   120.09    -9.59  1.70e+00  3.18e+01   5.6*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   125.30   -11.20  2.00e+00  3.13e+01   5.6*sigma
   A  82  THR  N
   A  82  THR  CA
   A  82  THR  C         111.00   126.64   -15.64  2.80e+00  3.12e+01   5.6*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   131.74   -10.04  1.80e+00  3.11e+01   5.6*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40   102.38     8.02  1.50e+00  2.86e+01   5.3*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   119.54    -9.04  1.70e+00  2.83e+01   5.3*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.80    -5.20  1.00e+00  2.70e+01   5.2*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   100.48     9.62  1.90e+00  2.56e+01   5.1*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10   100.64     9.46  1.90e+00  2.48e+01   5.0*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   130.65    -8.95  1.80e+00  2.47e+01   5.0*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.54    -4.94  1.00e+00  2.44e+01   4.9*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   106.39     9.81  2.00e+00  2.40e+01   4.9*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   118.69    -8.29  1.70e+00  2.38e+01   4.9*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.33    -9.73  2.00e+00  2.36e+01   4.9*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   102.29     8.21  1.70e+00  2.33e+01   4.8*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   119.26    -9.16  1.90e+00  2.32e+01   4.8*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00    97.91    13.09  2.80e+00  2.19e+01   4.7*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   130.04    -8.34  1.80e+00  2.15e+01   4.6*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  CB        110.50   102.70     7.80  1.70e+00  2.11e+01   4.6*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG2       110.50   118.25    -7.75  1.70e+00  2.08e+01   4.6*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   129.78    -8.08  1.80e+00  2.02e+01   4.5*sigma
   A 122  ILE  C
   A 122  ILE  CA
   A 122  ILE  CB        111.60   120.57    -8.97  2.00e+00  2.01e+01   4.5*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00   123.47   -12.47  2.80e+00  1.98e+01   4.5*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O         120.80   128.11    -7.31  1.70e+00  1.85e+01   4.3*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   107.71    -4.71  1.10e+00  1.84e+01   4.3*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   129.28    -7.58  1.80e+00  1.77e+01   4.2*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.20    -5.80  1.40e+00  1.72e+01   4.1*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.91     5.29  1.30e+00  1.66e+01   4.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N         116.20   108.12     8.08  2.00e+00  1.63e+01   4.0*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   102.49     7.61  1.90e+00  1.60e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   21.321 (Z= 11.845)
  Mean delta:    2.944 (Z=  1.573)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00    55.93   124.07  5.00e+00  6.16e+02  24.8*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    78.26   101.74  5.00e+00  4.14e+02  20.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -86.42   -93.58  5.00e+00  3.50e+02  18.7*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   106.15    73.85  5.00e+00  2.18e+02  14.8*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -107.79   -72.21  5.00e+00  2.09e+02  14.4*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   111.48    68.52  5.00e+00  1.88e+02  13.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -112.50   -67.50  5.00e+00  1.82e+02  13.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -113.08   -66.92  5.00e+00  1.79e+02  13.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -116.75   -63.25  5.00e+00  1.60e+02  12.6*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   118.39    61.61  5.00e+00  1.52e+02  12.3*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   118.42    61.58  5.00e+00  1.52e+02  12.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   123.39    56.61  5.00e+00  1.28e+02  11.3*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -128.50   -51.50  5.00e+00  1.06e+02  10.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -134.96   -45.04  5.00e+00  8.11e+01   9.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -137.90   -42.10  5.00e+00  7.09e+01   8.4*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -143.38   -36.62  5.00e+00  5.36e+01   7.3*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   146.79    33.21  5.00e+00  4.41e+01   6.6*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   148.44    31.56  5.00e+00  3.98e+01   6.3*sigma
   A 100  GLN  CA
   A 100  GLN  C
   A 101  LYS  N
   A 101  LYS  CA        180.00   149.50    30.50  5.00e+00  3.72e+01   6.1*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   151.79    28.21  5.00e+00  3.18e+01   5.6*sigma
   A  38  ILE  CA
   A  38  ILE  C
   A  39  LEU  N
   A  39  LEU  CA        180.00   153.62    26.38  5.00e+00  2.78e+01   5.3*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   157.29    22.71  5.00e+00  2.06e+01   4.5*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   157.72    22.28  5.00e+00  1.99e+01   4.5*sigma
   A  44  ASP  CA
   A  44  ASP  C
   A  45  PHE  N
   A  45  PHE  CA        180.00   159.37    20.63  5.00e+00  1.70e+01   4.1*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   159.99    20.01  5.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.001
  Max. delta:  124.075
  Mean delta:   21.083

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.87     5.40  2.00e-01  7.29e+02  27.0*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.79     5.34  2.00e-01  7.13e+02  26.7*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.82     5.33  2.00e-01  7.11e+02  26.7*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.76     5.27  2.00e-01  6.95e+02  26.4*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.20     4.84  2.00e-01  5.86e+02  24.2*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.30     4.81  2.00e-01  5.79e+02  24.1*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.94     4.45  2.00e-01  4.94e+02  22.2*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -1.79     4.43  2.00e-01  4.91e+02  22.2*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.91     4.34  2.00e-01  4.72e+02  21.7*sigma
   A  82  THR  CA
   A  82  THR  N
   A  82  THR  C
   A  82  THR  CB          2.53     0.76     1.76  2.00e-01  7.77e+01   8.8*sigma

  Min. delta:    0.000
  Max. delta:    5.400
  Mean delta:    1.136

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.155       0.301      481.27  15.1*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O
   A 124  ALA  N             0.069       0.119       47.56   6.0*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O
   A 125  LYS  N             0.065       0.112       42.09   5.6*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O
   A 126  VAL  N             0.057       0.098       31.97   4.9*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O
   A  91  TYR  N             0.050       0.086       24.85   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.155
  Mean delta:    0.023

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 127  ARG  HA , Angle C-CA-HA, observed: 96.305, delta from target: 12.695
   A 122  ILE  HB , Angle CA-CB-HB, observed: 95.543, delta from target: 13.457
   A 123  GLU  HA , Angle N-CA-HA, observed: 124.323, delta from target: -14.323
   A  90  SER  HA , Angle CB-CA-HA, observed: 94.274, delta from target: 14.726
   A  79  LYS  HA , Angle CB-CA-HA, observed: 124.058, delta from target: -15.058
   A 122  ILE  HA , Angle N-CA-HA, observed: 125.290, delta from target: -15.290
   A  89  TYR  HA , Angle CB-CA-HA, observed: 93.577, delta from target: 15.423
   A 124  ALA  HA , Angle C-CA-HA, observed: 92.514, delta from target: 16.486
   A  77  ILE  HA , Angle C-CA-HA, observed: 92.292, delta from target: 16.708
   A  81  TYR  HA , Angle N-CA-HA, observed: 91.381, delta from target: 18.619
   A  82  THR  HA , Angle N-CA-HA, observed: 89.712, delta from target: 20.288
   A  78  ILE  HB , Angle CA-CB-HB, observed: 88.015, delta from target: 20.985
   A  82  THR  HA , Angle C-CA-HA, observed: 78.026, delta from target: 30.974

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.124   2242  Z= 0.648
    Angle     :  2.617  30.974   4079  Z= 1.154
    Chirality :  1.136   5.400    176
    Planarity :  0.017   0.146    327
    Dihedral  : 16.978 124.075    769
    Min Nonbonded Distance : 1.493
  
  Molprobity Statistics.
    All-atom Clashscore : 19.84
    Ramachandran Plot:
      Outliers : 10.22 %
      Allowed  : 11.68 %
      Favored  : 78.10 %
    Rotamer:
      Outliers :  9.68 %
      Allowed  :  2.42 %
      Favored  : 87.90 %
    Cbeta Deviations : 13.64 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 13.74 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.62 (0.64), residues: 137
    helix: -2.70 (0.43), residues: 77
    sheet:  None (None), residues: 0
    loop : -1.77 (0.87), residues: 60
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.003   HIS A 135 
   PHE   0.057   0.010   PHE A  45 
   TYR   0.379   0.032   TYR A  81 
   ARG   0.044   0.008   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.003   HIS A 135 
   PHE   0.038   0.010   PHE A  45 
   TYR   0.301   0.038   TYR A  81 
   ARG   0.004   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.55    -0.10  1.60e-02  3.82e+01   6.2*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.57    -0.11  1.90e-02  3.56e+01   6.0*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.65    -0.12  2.10e-02  3.50e+01   5.9*sigma
   A 125  LYS  N
   A 125  LYS  CA          1.46     1.57    -0.11  1.90e-02  3.23e+01   5.7*sigma
   A  93  LEU  N
   A  93  LEU  CA          1.46     1.36     0.10  1.90e-02  2.79e+01   5.3*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.26     0.07  1.40e-02  2.70e+01   5.2*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.42     0.10  2.10e-02  2.49e+01   5.0*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.63    -0.10  2.10e-02  2.32e+01   4.8*sigma
   A  88  ASP  C
   A  89  TYR  N           1.33     1.40    -0.07  1.40e-02  2.23e+01   4.7*sigma
   A  89  TYR  N
   A  89  TYR  CA          1.46     1.53    -0.08  1.90e-02  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.124 (Z=  6.182)
  Mean delta:    0.018 (Z=  0.943)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50    90.37    21.13  1.70e+00  1.55e+02  12.4*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   131.98   -21.88  1.90e+00  1.33e+02  11.5*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20    94.84    21.36  2.00e+00  1.14e+02  10.7*sigma
   A 126  VAL  O
   A 126  VAL  C
   A 127  ARG  N         123.00   106.05    16.95  1.60e+00  1.12e+02  10.6*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   103.07    18.63  1.80e+00  1.07e+02  10.3*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   103.61    18.09  1.80e+00  1.01e+02  10.1*sigma
   A  93  LEU  CD1
   A  93  LEU  CG
   A  93  LEU  CD2       110.80   132.84   -22.04  2.20e+00  1.00e+02  10.0*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   104.68    17.02  1.80e+00  8.94e+01   9.5*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   138.44   -16.74  1.80e+00  8.65e+01   9.3*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30    93.18    16.12  2.00e+00  6.50e+01   8.1*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   110.82    12.18  1.60e+00  5.80e+01   7.6*sigma
   A  79  LYS  CG
   A  79  LYS  CD
   A  79  LYS  CE        111.30   128.61   -17.31  2.30e+00  5.67e+01   7.5*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   135.01   -13.31  1.80e+00  5.47e+01   7.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.96   -11.06  1.50e+00  5.44e+01   7.4*sigma
   A 119  LEU  C
   A 119  LEU  CA
   A 119  LEU  CB        110.10   123.95   -13.85  1.90e+00  5.31e+01   7.3*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   111.44    11.56  1.60e+00  5.22e+01   7.2*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   130.48   -14.28  2.00e+00  5.10e+01   7.1*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   123.20   -13.10  1.90e+00  4.76e+01   6.9*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   121.74   -11.24  1.70e+00  4.37e+01   6.6*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   100.65    10.85  1.70e+00  4.07e+01   6.4*sigma
   A 128  MET  CA
   A 128  MET  CB
   A 128  MET  CG        114.10   125.84   -11.74  2.00e+00  3.45e+01   5.9*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    94.69    16.31  2.80e+00  3.39e+01   5.8*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.08   -10.38  1.80e+00  3.32e+01   5.8*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   132.01   -10.31  1.80e+00  3.28e+01   5.7*sigma
   A  88  ASP  O
   A  88  ASP  C
   A  89  TYR  N         123.00   113.97     9.03  1.60e+00  3.19e+01   5.6*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.12    -5.52  1.00e+00  3.05e+01   5.5*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   131.59    -9.89  1.80e+00  3.02e+01   5.5*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  C         111.00   126.35   -15.35  2.80e+00  3.01e+01   5.5*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   101.21     9.29  1.70e+00  2.98e+01   5.5*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.41    -9.71  1.80e+00  2.91e+01   5.4*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   131.39    -9.69  1.80e+00  2.90e+01   5.4*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   112.10     9.60  1.80e+00  2.85e+01   5.3*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   131.30    -9.60  1.80e+00  2.84e+01   5.3*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80    99.37    11.43  2.20e+00  2.70e+01   5.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   126.54   -10.34  2.00e+00  2.67e+01   5.2*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   105.91    10.29  2.00e+00  2.65e+01   5.1*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   122.97   -11.67  2.30e+00  2.58e+01   5.1*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   119.58    -9.48  1.90e+00  2.49e+01   5.0*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   129.04    -8.24  1.70e+00  2.35e+01   4.8*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   106.52     9.68  2.00e+00  2.34e+01   4.8*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   119.28    -9.18  1.90e+00  2.34e+01   4.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   106.61     9.59  2.00e+00  2.30e+01   4.8*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   118.58    -8.08  1.70e+00  2.26e+01   4.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.02    -9.42  2.00e+00  2.22e+01   4.7*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   130.12    -8.42  1.80e+00  2.19e+01   4.7*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N         116.20   125.36    -9.16  2.00e+00  2.10e+01   4.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O         120.80   128.48    -7.68  1.70e+00  2.04e+01   4.5*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   122.03    -8.13  1.80e+00  2.04e+01   4.5*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   125.22    -9.02  2.00e+00  2.03e+01   4.5*sigma
   A 115  ALA  N
   A 115  ALA  CA
   A 115  ALA  CB        110.40   103.67     6.73  1.50e+00  2.02e+01   4.5*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00   123.43   -12.43  2.80e+00  1.97e+01   4.4*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   121.82    -7.92  1.80e+00  1.94e+01   4.4*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.29     4.31  1.00e+00  1.86e+01   4.3*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   116.92    -6.42  1.50e+00  1.83e+01   4.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   107.68     8.52  2.00e+00  1.81e+01   4.3*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   129.33    -7.63  1.80e+00  1.80e+01   4.2*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N         116.20   107.78     8.42  2.00e+00  1.77e+01   4.2*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   114.18     7.52  1.80e+00  1.75e+01   4.2*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   117.50    -7.10  1.70e+00  1.74e+01   4.2*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.78     5.42  1.30e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.45     4.15  1.00e+00  1.72e+01   4.1*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   116.70    -4.10  1.00e+00  1.68e+01   4.1*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.56     4.04  1.00e+00  1.63e+01   4.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N         116.20   108.13     8.07  2.00e+00  1.63e+01   4.0*sigma
   A  78  ILE  CG1
   A  78  ILE  CB
   A  78  ILE  CG2       110.70    98.64    12.06  3.00e+00  1.62e+01   4.0*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   122.21   -11.21  2.80e+00  1.60e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   22.038 (Z= 12.431)
  Mean delta:    3.310 (Z=  1.756)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00    56.22   123.78  5.00e+00  6.13e+02  24.8*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00    66.21   113.79  5.00e+00  5.18e+02  22.8*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    68.09   111.91  5.00e+00  5.01e+02  22.4*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   -77.11  -102.89  5.00e+00  4.23e+02  20.6*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -83.69   -96.31  5.00e+00  3.71e+02  19.3*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   -88.02   -91.98  5.00e+00  3.38e+02  18.4*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    88.42    91.58  5.00e+00  3.35e+02  18.3*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00    92.08    87.92  5.00e+00  3.09e+02  17.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    98.94    81.06  5.00e+00  2.63e+02  16.2*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   100.33    79.67  5.00e+00  2.54e+02  15.9*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   101.39    78.61  5.00e+00  2.47e+02  15.7*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   101.92    78.08  5.00e+00  2.44e+02  15.6*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   105.18    74.82  5.00e+00  2.24e+02  15.0*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   109.65    70.35  5.00e+00  1.98e+02  14.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -111.62   -68.38  5.00e+00  1.87e+02  13.7*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   120.61    59.39  5.00e+00  1.41e+02  11.9*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   125.78    54.22  5.00e+00  1.18e+02  10.8*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   128.23    51.77  5.00e+00  1.07e+02  10.4*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -138.06   -41.94  5.00e+00  7.04e+01   8.4*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00  -141.87   -38.13  5.00e+00  5.81e+01   7.6*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -148.12   -31.88  5.00e+00  4.07e+01   6.4*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -149.19   -30.81  5.00e+00  3.80e+01   6.2*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   152.97    27.03  5.00e+00  2.92e+01   5.4*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   154.62    25.38  5.00e+00  2.58e+01   5.1*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -159.00   -21.00  5.00e+00  1.76e+01   4.2*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00  -159.20   -20.80  5.00e+00  1.73e+01   4.2*sigma

  Min. delta:    0.029
  Max. delta:  123.783
  Mean delta:   23.673

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.53     6.04  2.00e-01  9.13e+02  30.2*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -3.08     5.63  2.00e-01  7.92e+02  28.1*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -3.14     5.58  2.00e-01  7.77e+02  27.9*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.70     5.34  2.00e-01  7.13e+02  26.7*sigma
   A 117  PRO  CA
   A 117  PRO  N
   A 117  PRO  C
   A 117  PRO  CB          2.72    -2.45     5.17  2.00e-01  6.69e+02  25.9*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -2.46     5.10  2.00e-01  6.51e+02  25.5*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.55     5.07  2.00e-01  6.41e+02  25.3*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.46     4.97  2.00e-01  6.18e+02  24.9*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.30     4.81  2.00e-01  5.80e+02  24.1*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.22     4.66  2.00e-01  5.42e+02  23.3*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -1.91     4.42  2.00e-01  4.88e+02  22.1*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -1.82     4.33  2.00e-01  4.69e+02  21.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.09     3.53  2.00e-01  3.11e+02  17.6*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51    -0.71     3.22  2.00e-01  2.60e+02  16.1*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     1.50     1.01  2.00e-01  2.54e+01   5.0*sigma

  Min. delta:    0.000
  Max. delta:    6.043
  Mean delta:    1.394

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O
   A 125  LYS  N             0.060       0.104       36.27   5.2*sigma

  Min. delta:    0.000
  Max. delta:    0.102
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  78  ILE  HB , Angle CG1-CB-HB, observed: 121.136, delta from target: -12.136
   A 127  ARG  HA , Angle C-CA-HA, observed: 96.727, delta from target: 12.273
   A  93  LEU  HG , Angle CD2-CG-HG, observed: 95.598, delta from target: 12.402
   A  97  SER  HA , Angle C-CA-HA, observed: 96.203, delta from target: 12.797
   A  92  THR  HA , Angle N-CA-HA, observed: 96.230, delta from target: 13.770
   A  97  SER  HA , Angle N-CA-HA, observed: 95.413, delta from target: 14.587
   A  51  ILE  HA , Angle CB-CA-HA, observed: 94.312, delta from target: 14.688
   A  92  THR  HB , Angle CG2-CB-HB, observed: 122.934, delta from target: -14.934
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.611, delta from target: 15.389
   A 128  MET  HA , Angle N-CA-HA, observed: 126.199, delta from target: -16.199
   A  93  LEU  HG , Angle CB-CG-HG, observed: 129.477, delta from target: -20.477
   A 128  MET  HA , Angle CB-CA-HA, observed: 87.586, delta from target: 21.414
   A  81  TYR  HA , Angle C-CA-HA, observed: 84.229, delta from target: 24.771
   A  81  TYR  HA , Angle N-CA-HA, observed: 82.248, delta from target: 27.752

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.124   2242  Z= 0.672
    Angle     :  2.809  27.752   4079  Z= 1.258
    Chirality :  1.394   6.043    176
    Planarity :  0.015   0.102    327
    Dihedral  : 18.953 123.783    769
    Min Nonbonded Distance : 1.603
  
  Molprobity Statistics.
    All-atom Clashscore : 28.85
    Ramachandran Plot:
      Outliers : 12.41 %
      Allowed  :  8.76 %
      Favored  : 78.83 %
    Rotamer:
      Outliers : 10.48 %
      Allowed  :  5.65 %
      Favored  : 83.87 %
    Cbeta Deviations : 12.88 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 16.03 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.42 (0.66), residues: 137
    helix: -1.80 (0.50), residues: 69
    sheet:  None (None), residues: 0
    loop : -2.80 (0.81), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.019   0.004   HIS A  43 
   PHE   0.072   0.010   PHE A  67 
   TYR   0.119   0.018   TYR A  12 
   ARG   0.025   0.006   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.019   0.004   HIS A  43 
   PHE   0.052   0.011   PHE A  67 
   TYR   0.098   0.018   TYR A  12 
   ARG   0.010   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  91.24 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =     8
  Clashscore            =  13.98
  RMS(bonds)            =   0.0100
  RMS(angles)           =   2.28
  MolProbity score      =   2.78

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =  10.22 %
                favored =  78.10 %
  Rotamer outliers      =   9.68 %
  C-beta deviations     =    18
  Clashscore            =  19.84
  RMS(bonds)            =   0.0123
  RMS(angles)           =   2.62
  MolProbity score      =   3.30

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =  12.41 %
                favored =  78.83 %
  Rotamer outliers      =  10.48 %
  C-beta deviations     =    17
  Clashscore            =  28.85
  RMS(bonds)            =   0.0129
  RMS(angles)           =   2.81
  MolProbity score      =   3.47

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.80 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.71    -0.19  1.80e-02  1.15e+02  10.7*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.64    -0.18  1.90e-02  9.04e+01   9.5*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     1.60    -0.14  1.90e-02  5.70e+01   7.6*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.43    -0.11  1.40e-02  5.64e+01   7.5*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.59    -0.13  1.90e-02  4.78e+01   6.9*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     1.57    -0.11  1.90e-02  3.18e+01   5.6*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.62    -0.09  2.10e-02  1.95e+01   4.4*sigma
   A 127  ARG  CA
   A 127  ARG  C           1.52     1.61    -0.09  2.10e-02  1.78e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.193 (Z= 10.739)
  Mean delta:    0.019 (Z=  0.987)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    78.70    32.30  2.80e+00  1.33e+02  11.5*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   131.93   -21.83  1.90e+00  1.32e+02  11.5*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   138.99   -17.29  1.80e+00  9.23e+01   9.6*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   138.81   -17.11  1.80e+00  9.04e+01   9.5*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  CB        110.50    95.24    15.26  1.70e+00  8.06e+01   9.0*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50    96.52    14.98  1.70e+00  7.77e+01   8.8*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    97.93    13.57  1.70e+00  6.37e+01   8.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.61   -11.71  1.50e+00  6.09e+01   7.8*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   124.59   -14.49  1.90e+00  5.81e+01   7.6*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   130.87   -14.67  2.00e+00  5.38e+01   7.3*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   120.47    -9.97  1.50e+00  4.42e+01   6.6*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   124.09   -12.49  2.00e+00  3.90e+01   6.2*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   120.62   -10.12  1.70e+00  3.54e+01   6.0*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.37   -10.67  1.80e+00  3.51e+01   5.9*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   132.29   -10.59  1.80e+00  3.46e+01   5.9*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   104.45    11.75  2.00e+00  3.45e+01   5.9*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00   127.06   -16.06  2.80e+00  3.29e+01   5.7*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   120.03    -9.63  1.70e+00  3.21e+01   5.7*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   131.17    -9.47  1.80e+00  2.77e+01   5.3*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50   102.87     8.63  1.70e+00  2.58e+01   5.1*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   119.02    -8.52  1.70e+00  2.51e+01   5.0*sigma
   A  43  HIS  CA
   A  43  HIS  CB
   A  43  HIS  CG        113.80   118.67    -4.87  1.00e+00  2.37e+01   4.9*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   130.38    -8.68  1.80e+00  2.33e+01   4.8*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   115.48     7.52  1.60e+00  2.21e+01   4.7*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   113.81     7.89  1.80e+00  1.92e+01   4.4*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   129.57    -7.87  1.80e+00  1.91e+01   4.4*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   116.86    -4.26  1.00e+00  1.82e+01   4.3*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.28    -5.88  1.40e+00  1.76e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.75e+01   4.2*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   119.90    -8.30  2.00e+00  1.72e+01   4.1*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   117.52    -7.02  1.70e+00  1.70e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.79     7.01  1.70e+00  1.70e+01   4.1*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.52     4.08  1.00e+00  1.67e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.53     4.07  1.00e+00  1.66e+01   4.1*sigma
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        121.70   129.03    -7.33  1.80e+00  1.66e+01   4.1*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG1       110.40   117.30    -6.90  1.70e+00  1.65e+01   4.1*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   128.92    -7.22  1.80e+00  1.61e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:   32.301 (Z= 11.536)
  Mean delta:    2.870 (Z=  1.532)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    68.06   111.94  5.00e+00  5.01e+02  22.4*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   -68.39  -111.61  5.00e+00  4.98e+02  22.3*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00    81.25    98.75  5.00e+00  3.90e+02  19.7*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    86.12    93.88  5.00e+00  3.53e+02  18.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    94.41    85.59  5.00e+00  2.93e+02  17.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   101.59    78.41  5.00e+00  2.46e+02  15.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   102.37    77.63  5.00e+00  2.41e+02  15.5*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   104.18    75.82  5.00e+00  2.30e+02  15.2*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   128.80    51.20  5.00e+00  1.05e+02  10.2*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -132.97   -47.03  5.00e+00  8.85e+01   9.4*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -139.13   -40.87  5.00e+00  6.68e+01   8.2*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   141.01    38.99  5.00e+00  6.08e+01   7.8*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA          0.00    34.88   -34.88  5.00e+00  4.87e+01   7.0*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   145.88    34.12  5.00e+00  4.66e+01   6.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   150.09    29.91  5.00e+00  3.58e+01   6.0*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   151.23    28.77  5.00e+00  3.31e+01   5.8*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   153.41    26.59  5.00e+00  2.83e+01   5.3*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   153.70    26.30  5.00e+00  2.77e+01   5.3*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -154.65   -25.35  5.00e+00  2.57e+01   5.1*sigma
   A 111  TYR  CA
   A 111  TYR  C
   A 112  VAL  N
   A 112  VAL  CA        180.00   155.99    24.01  5.00e+00  2.31e+01   4.8*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -157.02   -22.98  5.00e+00  2.11e+01   4.6*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00  -159.35   -20.65  5.00e+00  1.71e+01   4.1*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00  -159.64   -20.36  5.00e+00  1.66e+01   4.1*sigma
   A  47  ASP  CA
   A  47  ASP  C
   A  48  ALA  N
   A  48  ALA  CA        180.00   159.76    20.24  5.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.016
  Max. delta:  111.940
  Mean delta:   19.723

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.66     5.22  2.00e-01  6.80e+02  26.1*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.69     5.20  2.00e-01  6.75e+02  26.0*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -1.98     4.49  2.00e-01  5.04e+02  22.5*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51    -1.39     3.90  2.00e-01  3.80e+02  19.5*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.77     3.20  2.00e-01  2.57e+02  16.0*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.23     1.28  2.00e-01  4.10e+01   6.4*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53     1.31     1.21  2.00e-01  3.67e+01   6.1*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43     3.39    -0.96  2.00e-01  2.31e+01   4.8*sigma

  Min. delta:    0.001
  Max. delta:    5.216
  Mean delta:    0.788

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.064       0.115       82.91   5.7*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.046       0.083       43.14   4.2*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  91  TYR  O
   A  92  THR  N             0.047       0.082       22.25   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.116
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  91  TYR  HA , Angle CB-CA-HA, observed: 95.640, delta from target: 13.360
   A  77  ILE  HA , Angle CB-CA-HA, observed: 95.241, delta from target: 13.759
   A  91  TYR  HA , Angle C-CA-HA, observed: 92.011, delta from target: 16.989
   A  51  ILE  HA , Angle C-CA-HA, observed: 88.151, delta from target: 20.849
   A  51  ILE  HA , Angle CB-CA-HA, observed: 85.949, delta from target: 23.051
   A 127  ARG  HA , Angle N-CA-HA, observed: 86.110, delta from target: 23.890
   A  92  THR  HA , Angle N-CA-HA, observed: 81.481, delta from target: 28.519
   A 128  MET  HA , Angle N-CA-HA, observed: 143.814, delta from target: -33.814

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.193   2242  Z= 0.702
    Angle     :  2.568  33.814   4079  Z= 1.128
    Chirality :  0.788   5.216    176
    Planarity :  0.012   0.091    327
    Dihedral  : 15.973 111.940    769
    Min Nonbonded Distance : 1.133
  
  Molprobity Statistics.
    All-atom Clashscore : 14.43
    Ramachandran Plot:
      Outliers : 10.95 %
      Allowed  :  7.30 %
      Favored  : 81.75 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  3.23 %
      Favored  : 91.13 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 10.69 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.17 (0.65), residues: 137
    helix: -1.85 (0.51), residues: 63
    sheet:  None (None), residues: 0
    loop : -2.36 (0.75), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.068   0.011   PHE A  45 
   TYR   0.162   0.024   TYR A  91 
   ARG   0.096   0.012   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.047   0.012   PHE A  45 
   TYR   0.127   0.027   TYR A  91 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.036 (Z=  2.935)
  Mean delta:    0.013 (Z=  0.677)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 135  HIS  CA
   A 135  HIS  CB
   A 135  HIS  CG        113.80   118.85    -5.05  1.00e+00  2.55e+01   5.0*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   117.61     4.99  1.00e+00  2.49e+01   5.0*sigma
   A  82  THR  CA
   A  82  THR  CB
   A  82  THR  OG1       109.60   116.82    -7.22  1.50e+00  2.32e+01   4.8*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   129.83    -8.13  1.80e+00  2.04e+01   4.5*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.53     4.07  1.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.006 (Z=  0.003)
  Max. delta:    8.460 (Z=  5.048)
  Mean delta:    1.982 (Z=  1.083)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   140.95    39.05  5.00e+00  6.10e+01   7.8*sigma
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00  -148.80   -31.20  5.00e+00  3.89e+01   6.2*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   154.91    25.09  5.00e+00  2.52e+01   5.0*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -159.53   -20.47  5.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.018
  Max. delta:   88.963
  Mean delta:   18.589

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:    0.398
  Mean delta:    0.098

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  ND1
   A 135  HIS  CD2
   A 135  HIS  CE1
   A 135  HIS  NE2           0.060       0.081       54.48   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.075
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.036   2242  Z= 0.482
    Angle     :  1.799   8.460   4079  Z= 0.798
    Chirality :  0.098   0.398    176
    Planarity :  0.013   0.080    327
    Dihedral  : 14.939  88.963    769
    Min Nonbonded Distance : 1.734
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  : 10.22 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  9.68 %
      Favored  : 83.06 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 1.53 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.08 (0.65), residues: 137
    helix: -1.22 (0.53), residues: 62
    sheet:  None (None), residues: 0
    loop : -1.49 (0.73), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A 135 
   PHE   0.076   0.018   PHE A  45 
   TYR   0.162   0.029   TYR A  89 
   ARG   0.059   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A 135 
   PHE   0.054   0.015   PHE A  45 
   TYR   0.130   0.029   TYR A  12 
   ARG   0.008   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 110
        1.23 -     1.43: 361
        1.43 -     1.62: 661
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" N   GLY A  87 "
       model="  13" pdb=" CA  GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.451  1.523 -0.072 1.60e-02 3.91e+03 2.01e+01
  bond model="  13" pdb=" CA  GLY A  87 "
       model="  13" pdb=" C   GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.516  1.585 -0.069 1.80e-02 3.09e+03 1.46e+01
  bond model="  13" pdb=" N   ILE A  86 "
       model="  13" pdb=" CA  ILE A  86 "
    ideal  model  delta    sigma   weight residual
    1.458  1.522 -0.064 1.90e-02 2.77e+03 1.12e+01
  bond model="  13" pdb=" CA  ILE A  86 "
       model="  13" pdb=" C   ILE A  86 "
    ideal  model  delta    sigma   weight residual
    1.525  1.592 -0.067 2.10e-02 2.27e+03 1.03e+01
  bond model="  13" pdb=" C   ILE A  86 "
       model="  13" pdb=" N   GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.329  1.371 -0.042 1.40e-02 5.10e+03 9.05e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       96.51 -   103.36: 26
      103.36 -   110.22: 2139
      110.22 -   117.07: 869
      117.07 -   123.93: 916
      123.93 -   130.78: 129
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" OE1 GLN A  66 "
        model="  13" pdb=" CD  GLN A  66 "
        model="  13" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.27    5.33 1.00e+00 1.00e+00 2.84e+01
  angle model="  13" pdb=" C   ILE A  71 "
        model="  13" pdb=" N   ASN A  72 "
        model="  13" pdb=" CA  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     121.70  130.78   -9.08 1.80e+00 3.09e-01 2.55e+01
  angle model="  13" pdb=" CA  HIS A 138 "
        model="  13" pdb=" CB  HIS A 138 "
        model="  13" pdb=" CG  HIS A 138 "
      ideal   model   delta    sigma   weight residual
     113.80  108.86    4.94 1.00e+00 1.00e+00 2.44e+01
  angle model="  13" pdb=" C   THR A  83 "
        model="  13" pdb=" N   GLU A  84 "
        model="  13" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  129.91   -8.21 1.80e+00 3.09e-01 2.08e+01
  angle model="  13" pdb=" N   ASN A  72 "
        model="  13" pdb=" CA  ASN A  72 "
        model="  13" pdb=" HA  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     110.00   96.51   13.49 3.00e+00 1.11e-01 2.02e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.84: 960
       21.84 -    43.69: 60
       43.69 -    65.53: 10
       65.53 -    87.38: 1
       87.38 -   109.22: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  13" pdb=" CA  GLY A  73 "
           model="  13" pdb=" C   GLY A  73 "
           model="  13" pdb=" N   ASP A  74 "
           model="  13" pdb=" CA  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -70.78 -109.22     0      5.00e+00 4.00e-02 4.77e+02
  dihedral model="  13" pdb=" CA  ASN A  72 "
           model="  13" pdb=" C   ASN A  72 "
           model="  13" pdb=" N   GLY A  73 "
           model="  13" pdb=" CA  GLY A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.57   28.43     0      5.00e+00 4.00e-02 3.23e+01
  dihedral model="  13" pdb=" N   ASN A  72 "
           model="  13" pdb=" C   ASN A  72 "
           model="  13" pdb=" CA  ASN A  72 "
           model="  13" pdb=" CB  ASN A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.42  -13.62     0      2.50e+00 1.60e-01 2.97e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 130
       0.122 -    0.244: 39
       0.244 -    0.365: 6
       0.365 -    0.487: 0
       0.487 -    0.608: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  ASN A  72 "
            model="  13" pdb=" N   ASN A  72 "
            model="  13" pdb=" C   ASN A  72 "
            model="  13" pdb=" CB  ASN A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.90    0.61 2.00e-01 2.50e+01 9.25e+00
  chirality model="  13" pdb=" CA  VAL A 104 "
            model="  13" pdb=" N   VAL A 104 "
            model="  13" pdb=" C   VAL A 104 "
            model="  13" pdb=" CB  VAL A 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.11    0.33 2.00e-01 2.50e+01 2.80e+00
  chirality model="  13" pdb=" CA  ASP A 118 "
            model="  13" pdb=" N   ASP A 118 "
            model="  13" pdb=" C   ASP A 118 "
            model="  13" pdb=" CB  ASP A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  89 "   -0.501 2.00e-02 2.50e+03   1.98e-01 1.18e+03
        model="  13" pdb=" CG  TYR A  89 "    0.058 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  89 "    0.081 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  89 "    0.154 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  89 "    0.042 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  89 "   -0.015 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  89 "   -0.094 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  89 "   -0.193 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  89 "    0.123 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  89 "    0.325 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  89 "    0.106 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  89 "   -0.084 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  12 "    0.162 2.00e-02 2.50e+03   7.46e-02 1.67e+02
        model="  13" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  12 "   -0.037 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  12 "   -0.031 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  12 "    0.155 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  12 "   -0.072 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  12 "   -0.045 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  12 "   -0.037 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  12 "   -0.065 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A 105 "   -0.139 2.00e-02 2.50e+03   7.38e-02 1.63e+02
        model="  13" pdb=" CG  TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A 105 "    0.039 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A 105 "    0.012 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A 105 "    0.014 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A 105 "    0.039 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A 105 "   -0.033 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A 105 "   -0.151 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A 105 "    0.082 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A 105 "    0.004 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A 105 "    0.028 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A 105 "    0.106 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 193
        2.23 -     2.82: 4477
        2.82 -     3.41: 6006
        3.41 -     4.01: 7148
        4.01 -     4.60: 10777
  Nonbonded interactions: 28601
  Sorted by model distance:
  nonbonded model="  13" pdb=" H   GLY A  73 "
            model="  13" pdb=" HB2 ASP A  74 "
     model   vdw
     1.632 2.270
  nonbonded model="  13" pdb=" OD2 ASP A  36 "
            model="  13" pdb=" HZ1 LYS A  40 "
     model   vdw
     1.719 1.850
  nonbonded model="  13" pdb=" HB3 ASP A  74 "
            model="  13" pdb=" H   SER A  76 "
     model   vdw
     1.741 2.270
  nonbonded model="  13" pdb=" OE1 GLU A  75 "
            model="  13" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.772 1.850
  nonbonded model="  13" pdb=" OE2 GLU A  24 "
            model="  13" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.773 1.850
  ... (remaining 28596 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A LEU    2": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   1.46 %
                favored =  88.32 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.80
  MolProbity score      =   2.62

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =  10.95 %
                favored =  81.75 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =    16
  Clashscore            =  14.43
  RMS(bonds)            =   0.0133
  RMS(angles)           =   2.57
  MolProbity score      =   2.95

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.758, 54.309, 47.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.62    -0.17  1.90e-02  7.57e+01   8.7*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.69    -0.17  2.10e-02  6.43e+01   8.0*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.56    -0.11  1.60e-02  4.38e+01   6.6*sigma
   A  77  ILE  N
   A  77  ILE  CA          1.46     1.58    -0.12  1.90e-02  4.13e+01   6.4*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.39    -0.06  1.40e-02  2.00e+01   4.5*sigma
   A  76  SER  CA
   A  76  SER  C           1.52     1.62    -0.09  2.10e-02  1.94e+01   4.4*sigma
   A  90  SER  N
   A  90  SER  CA          1.46     1.54    -0.08  1.90e-02  1.87e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.168 (Z=  8.702)
  Mean delta:    0.017 (Z=  0.901)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   169.46   -47.76  1.80e+00  7.04e+02  26.5*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   131.35   -20.85  1.70e+00  1.50e+02  12.3*sigma
   A  76  SER  N
   A  76  SER  CA
   A  76  SER  CB        110.50    90.68    19.82  1.70e+00  1.36e+02  11.7*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00   140.80   -29.80  2.80e+00  1.13e+02  10.6*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   130.72   -16.82  1.80e+00  8.74e+01   9.3*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   130.27   -16.17  2.00e+00  6.54e+01   8.1*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   126.16   -14.56  2.00e+00  5.30e+01   7.3*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   123.93   -13.83  1.90e+00  5.30e+01   7.3*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   125.93   -14.33  2.00e+00  5.13e+01   7.2*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.37   -12.67  1.80e+00  4.95e+01   7.0*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   121.81   -11.31  1.70e+00  4.43e+01   6.7*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  CB        111.50   100.56    10.94  1.70e+00  4.14e+01   6.4*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   133.22   -11.52  1.80e+00  4.10e+01   6.4*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    93.55    17.45  2.80e+00  3.88e+01   6.2*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   132.48   -10.78  1.80e+00  3.58e+01   6.0*sigma
   A  76  SER  O
   A  76  SER  C
   A  77  ILE  N         123.00   113.50     9.50  1.60e+00  3.53e+01   5.9*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   131.90   -10.20  1.80e+00  3.21e+01   5.7*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   102.35     9.15  1.70e+00  2.90e+01   5.4*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   105.58    10.62  2.00e+00  2.82e+01   5.3*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   131.16    -9.46  1.80e+00  2.76e+01   5.3*sigma
   A  86  ILE  C
   A  86  ILE  CA
   A  86  ILE  CB        111.60   121.98   -10.38  2.00e+00  2.69e+01   5.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   124.42    -7.52  1.50e+00  2.51e+01   5.0*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.44    -4.84  1.00e+00  2.34e+01   4.8*sigma
   A  76  SER  C
   A  76  SER  CA
   A  76  SER  CB        110.10   119.18    -9.08  1.90e+00  2.28e+01   4.8*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   118.52    -8.02  1.70e+00  2.22e+01   4.7*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00   124.16   -13.16  2.80e+00  2.21e+01   4.7*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N         116.20   107.03     9.17  2.00e+00  2.10e+01   4.6*sigma
   A  97  SER  O
   A  97  SER  C
   A  98  SER  N         123.00   129.82    -6.82  1.60e+00  1.82e+01   4.3*sigma
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        121.70   129.37    -7.67  1.80e+00  1.82e+01   4.3*sigma
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        121.70   129.32    -7.62  1.80e+00  1.79e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  C         111.00   122.35   -11.35  2.80e+00  1.64e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   47.764 (Z= 26.536)
  Mean delta:    3.038 (Z=  1.615)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    78.92   101.08  5.00e+00  4.09e+02  20.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00    90.72    89.28  5.00e+00  3.19e+02  17.9*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   102.22    77.78  5.00e+00  2.42e+02  15.6*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   111.58    68.42  5.00e+00  1.87e+02  13.7*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   117.15    62.85  5.00e+00  1.58e+02  12.6*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -119.01   -60.99  5.00e+00  1.49e+02  12.2*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   123.22    56.78  5.00e+00  1.29e+02  11.4*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   131.61    48.39  5.00e+00  9.37e+01   9.7*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -132.98   -47.02  5.00e+00  8.84e+01   9.4*sigma
   A   3  LEU  CA
   A   3  LEU  C
   A   4  ILE  N
   A   4  ILE  CA        180.00   144.26    35.74  5.00e+00  5.11e+01   7.1*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   146.43    33.57  5.00e+00  4.51e+01   6.7*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   151.86    28.14  5.00e+00  3.17e+01   5.6*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   154.84    25.16  5.00e+00  2.53e+01   5.0*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00  -157.29   -22.71  5.00e+00  2.06e+01   4.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA          0.00   -22.33    22.33  5.00e+00  1.99e+01   4.5*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   158.45    21.55  5.00e+00  1.86e+01   4.3*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -158.67   -21.33  5.00e+00  1.82e+01   4.3*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   158.93    21.07  5.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.012
  Max. delta:  101.084
  Mean delta:   17.159

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.78     5.29  2.00e-01  7.00e+02  26.4*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.64     5.28  2.00e-01  6.97e+02  26.4*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.54     5.05  2.00e-01  6.38e+02  25.3*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -2.26     4.77  2.00e-01  5.68e+02  23.8*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.21     4.72  2.00e-01  5.56e+02  23.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.43     2.87  2.00e-01  2.06e+02  14.3*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43     1.14     1.30  2.00e-01  4.20e+01   6.5*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64     1.57     1.08  2.00e-01  2.90e+01   5.4*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     1.56     0.95  2.00e-01  2.26e+01   4.8*sigma
   A  86  ILE  CA
   A  86  ILE  N
   A  86  ILE  C
   A  86  ILE  CB          2.43     1.52     0.91  2.00e-01  2.06e+01   4.5*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51     1.71     0.80  2.00e-01  1.61e+01   4.0*sigma

  Min. delta:    0.000
  Max. delta:    5.290
  Mean delta:    0.902

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.057       0.093       56.67   4.7*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.089       0.088      159.10   4.4*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.048       0.083       46.49   4.2*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.041       0.080       34.14   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.089
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="LYS A  79  conformer  : H 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  79  LYS  HA , Angle CB-CA-HA, observed: 94.700, delta from target: 14.300
   A  92  THR  HA , Angle N-CA-HA, observed: 95.665, delta from target: 14.335
   A  86  ILE  HA , Angle C-CA-HA, observed: 92.672, delta from target: 16.328
   A  51  ILE  HA , Angle N-CA-HA, observed: 127.518, delta from target: -17.518
   A  77  ILE  HA , Angle N-CA-HA, observed: 91.237, delta from target: 18.763
   A  76  SER  HA , Angle N-CA-HA, observed: 128.982, delta from target: -18.982
   A  78  ILE  HA , Angle C-CA-HA, observed: 88.725, delta from target: 20.275
   A  91  TYR  HA , Angle N-CA-HA, observed: 88.905, delta from target: 21.095
   A  79  LYS  HA , Angle C-CA-HA, observed: 131.908, delta from target: -22.908
   A  77  ILE  HB , Angle CG2-CB-HB, observed: 83.703, delta from target: 25.297
   A  51  ILE  HA , Angle C-CA-HA, observed: 82.703, delta from target: 26.297
   A  77  ILE  HA , Angle CB-CA-HA, observed: 141.756, delta from target: -32.756
   A  77  ILE  HA , Angle C-CA-HA, observed: 73.715, delta from target: 35.285
   A  51  ILE  HA , Angle CB-CA-HA, observed: 71.958, delta from target: 37.042

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.168   2241  Z= 0.641
    Angle     :  2.772  47.764   4077  Z= 1.205
    Chirality :  0.902   5.290    176
    Planarity :  0.011   0.075    326
    Dihedral  : 14.170 101.084    768
    Min Nonbonded Distance : 1.436
  
  Molprobity Statistics.
    All-atom Clashscore : 11.28
    Ramachandran Plot:
      Outliers :  7.30 %
      Allowed  :  8.03 %
      Favored  : 84.67 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  4.03 %
      Favored  : 91.94 %
    Cbeta Deviations :  9.85 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 8.40 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.08 (0.62), residues: 137
    helix: -1.23 (0.47), residues: 79
    sheet:  None (None), residues: 0
    loop : -3.23 (0.77), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.002   HIS A  43 
   PHE   0.137   0.021   PHE A  15 
   TYR   0.171   0.024   TYR A  91 
   ARG   0.035   0.005   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.002   HIS A  43 
   PHE   0.093   0.022   PHE A  15 
   TYR   0.163   0.029   TYR A  91 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   7.30 %
                favored =  84.67 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =    13
  Clashscore            =  11.28
  RMS(bonds)            =   0.0123
  RMS(angles)           =   2.77
  MolProbity score      =   2.69

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  ILE A  78 "
        model="   7" pdb=" CB  TYR A  91 "
        model="   7" pdb=" CB  LEU A  93 "
        model="   7" pdb=" CB  LYS A 125 "
        model="   7" pdb=" CB  VAL A 126 "
        model="   7" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  250

  Time building geometry restraints manager: 0.71 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.02, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (61.044, 49.859, 57.773, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 58
        1.23 -     1.43: 422
        1.43 -     1.62: 652
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" CA  VAL A 126 "
       model="   7" pdb=" C   VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.525  1.403  0.122 2.10e-02 2.27e+03 3.37e+01
  bond model="   7" pdb=" CA  LYS A 125 "
       model="   7" pdb=" C   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.525  1.416  0.109 2.10e-02 2.27e+03 2.72e+01
  bond model="   7" pdb=" N   LYS A 125 "
       model="   7" pdb=" CA  LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.545 -0.087 1.90e-02 2.77e+03 2.11e+01
  bond model="   7" pdb=" N   GLY A  80 "
       model="   7" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.520 -0.069 1.60e-02 3.91e+03 1.89e+01
  bond model="   7" pdb=" C   ALA A 124 "
       model="   7" pdb=" N   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.329  1.390 -0.061 1.40e-02 5.10e+03 1.88e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       80.19 -    92.63: 4
       92.63 -   105.07: 108
      105.07 -   117.51: 2953
      117.51 -   129.95: 1004
      129.95 -   142.39: 10
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" C   ASP A  88 "
        model="   7" pdb=" N   TYR A  89 "
        model="   7" pdb=" CA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     121.70  142.39  -20.69 1.80e+00 3.09e-01 1.32e+02
  angle model="   7" pdb=" C   TYR A  89 "
        model="   7" pdb=" N   SER A  90 "
        model="   7" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  104.34   17.36 1.80e+00 3.09e-01 9.30e+01
  angle model="   7" pdb=" CB  VAL A 126 "
        model="   7" pdb=" CA  VAL A 126 "
        model="   7" pdb=" HA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     109.00   80.19   28.81 3.00e+00 1.11e-01 9.22e+01
  angle model="   7" pdb=" N   SER A  90 "
        model="   7" pdb=" CA  SER A  90 "
        model="   7" pdb=" CB  SER A  90 "
      ideal   model   delta    sigma   weight residual
     110.50  126.49  -15.99 1.70e+00 3.46e-01 8.84e+01
  angle model="   7" pdb=" N   VAL A 126 "
        model="   7" pdb=" CA  VAL A 126 "
        model="   7" pdb=" CB  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     111.50  126.71  -15.21 1.70e+00 3.46e-01 8.00e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.22: 916
       20.22 -    40.44: 69
       40.44 -    60.67: 23
       60.67 -    80.89: 6
       80.89 -   101.11: 5
  Dihedral angle restraints: 1019
    sinusoidal: 562
      harmonic: 457
  Sorted by residual:
  dihedral model="   7" pdb=" CA  LEU A  93 "
           model="   7" pdb=" C   LEU A  93 "
           model="   7" pdb=" N   GLY A  94 "
           model="   7" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   78.89  101.11     0      5.00e+00 4.00e-02 4.09e+02
  dihedral model="   7" pdb=" CA  TYR A  89 "
           model="   7" pdb=" C   TYR A  89 "
           model="   7" pdb=" N   SER A  90 "
           model="   7" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   83.85   96.15     0      5.00e+00 4.00e-02 3.70e+02
  dihedral model="   7" pdb=" CA  LYS A 125 "
           model="   7" pdb=" C   LYS A 125 "
           model="   7" pdb=" N   VAL A 126 "
           model="   7" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  -88.41  -91.59     0      5.00e+00 4.00e-02 3.36e+02
  ... (remaining 1016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.054: 165
       1.054 -    2.108: 3
       2.108 -    3.162: 0
       3.162 -    4.215: 2
       4.215 -    5.269: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CB  ILE A  78 "
            model="   7" pdb=" CA  ILE A  78 "
            model="   7" pdb=" CG1 ILE A  78 "
            model="   7" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.62    5.27 2.00e-01 2.50e+01 6.94e+02
  chirality model="   7" pdb=" CA  LEU A  93 "
            model="   7" pdb=" N   LEU A  93 "
            model="   7" pdb=" C   LEU A  93 "
            model="   7" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.74    5.25 2.00e-01 2.50e+01 6.88e+02
  chirality model="   7" pdb=" CA  LYS A 125 "
            model="   7" pdb=" N   LYS A 125 "
            model="   7" pdb=" C   LYS A 125 "
            model="   7" pdb=" CB  LYS A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.35    4.86 2.00e-01 2.50e+01 5.91e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  PHE A  67 "   -0.143 2.00e-02 2.50e+03   5.70e-02 9.76e+01
        model="   7" pdb=" CG  PHE A  67 "    0.017 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 PHE A  67 "    0.042 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 PHE A  67 "    0.029 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 PHE A  67 "   -0.004 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 PHE A  67 "    0.008 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  PHE A  67 "   -0.025 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 PHE A  67 "    0.089 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 PHE A  67 "    0.052 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 PHE A  67 "   -0.020 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 PHE A  67 "    0.016 2.00e-02 2.50e+03
        model="   7" pdb=" HZ  PHE A  67 "   -0.062 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  50 "   -0.079 2.00e-02 2.50e+03   3.53e-02 3.73e+01
        model="   7" pdb=" CG  TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  50 "   -0.076 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  50 "    0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CA  LEU A  93 "    0.027 2.00e-02 2.50e+03   5.40e-02 2.92e+01
        model="   7" pdb=" C   LEU A  93 "   -0.093 2.00e-02 2.50e+03
        model="   7" pdb=" O   LEU A  93 "    0.036 2.00e-02 2.50e+03
        model="   7" pdb=" N   GLY A  94 "    0.030 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.44 -     2.07: 84
        2.07 -     2.70: 3360
        2.70 -     3.33: 6681
        3.33 -     3.97: 8055
        3.97 -     4.60: 12059
  Nonbonded interactions: 30239
  Sorted by model distance:
  nonbonded model="   7" pdb=" HB2 LEU A  93 "
            model="   7" pdb=" H   LEU A  99 "
     model   vdw
     1.436 2.270
  nonbonded model="   7" pdb=" HA  VAL A 126 "
            model="   7" pdb=" HB  VAL A 126 "
     model   vdw
     1.440 1.952
  nonbonded model="   7" pdb="HD12 LEU A  93 "
            model="   7" pdb=" H   GLY A  94 "
     model   vdw
     1.465 2.270
  nonbonded model="   7" pdb=" HG  LEU A  93 "
            model="   7" pdb=" H   ASP A  95 "
     model   vdw
     1.467 2.270
  nonbonded model="   7" pdb="HG22 ILE A  77 "
            model="   7" pdb=" H   ILE A  78 "
     model   vdw
     1.481 2.270
  ... (remaining 30234 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Time building chain proxies: 0.60, per 1000 atoms: 0.27
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.266, 63.264, 46.745, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  2.767)
  Mean delta:    0.013 (Z=  0.664)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   107.38     6.42  1.00e+00  4.12e+01   6.4*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.85     4.75  1.00e+00  2.26e+01   4.8*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.27     4.33  1.00e+00  1.87e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.35     4.25  1.00e+00  1.80e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.812 (Z=  6.420)
  Mean delta:    1.934 (Z=  1.067)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   157.83    22.17  5.00e+00  1.97e+01   4.4*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   159.40    20.60  5.00e+00  1.70e+01   4.1*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   159.41    20.59  5.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.040
  Max. delta:   62.455
  Mean delta:   15.643

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.244
  Mean delta:    0.089

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  67  PHE  CB
   A  67  PHE  CG
   A  67  PHE  CD1
   A  67  PHE  CD2
   A  67  PHE  CE1
   A  67  PHE  CE2
   A  67  PHE  CZ            0.148       0.242      385.27  12.1*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.116       0.100      268.75   5.0*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.120       0.091      289.40   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.148
  Mean delta:    0.023

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   15" pdbres="HIS A  43  conformer  : HE2, HD1 
   15" pdbres="HIS A 134  conformer  : HE2, HD1 
   15" pdbres="HIS A 135  conformer  : HE2, HD1 
   15" pdbres="HIS A 136  conformer  : HE2, HD1 
   15" pdbres="HIS A 137  conformer  : HE2, HD1 
   15" pdbres="HIS A 138  conformer  : HE2, HD1 
   15" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2242  Z= 0.473
    Angle     :  1.771   8.204   4079  Z= 0.788
    Chirality :  0.089   0.244    176
    Planarity :  0.018   0.160    327
    Dihedral  : 14.219  84.230    769
    Min Nonbonded Distance : 1.727
  
  Molprobity Statistics.
    All-atom Clashscore : 9.02
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  6.57 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  5.65 %
      Favored  : 91.94 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.33 (0.65), residues: 137
    helix: -1.46 (0.47), residues: 65
    sheet:  None (None), residues: 0
    loop : -1.58 (0.79), residues: 72
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.021   0.005   HIS A  43 
   PHE   0.366   0.061   PHE A  67 
   TYR   0.258   0.045   TYR A  91 
   ARG   0.114   0.014   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.021   0.005   HIS A  43 
   PHE   0.242   0.064   PHE A  67 
   TYR   0.212   0.048   TYR A  91 
   ARG   0.008   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 138  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.550)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.600 (Z=  1.352)
  Mean delta:    0.374 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   78.513
  Mean delta:   22.814

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.094
  Mean delta:    0.034

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.045
    Angle     :  0.980   4.837   4077  Z= 0.342
    Chirality :  0.034   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 17.697  78.513    768
    Min Nonbonded Distance : 1.517
  
  Molprobity Statistics.
    All-atom Clashscore : 18.94
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  : 16.79 %
      Favored  : 79.56 %
    Rotamer:
      Outliers : 21.77 %
      Allowed  : 25.00 %
      Favored  : 53.23 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.55 (0.43), residues: 137
    helix: -3.66 (0.41), residues: 73
    sheet:  None (None), residues: 0
    loop : -5.31 (0.42), residues: 64
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.001   0.000   PHE A  67 
   TYR   0.002   0.001   TYR A  50 
   ARG   0.001   0.000   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A  12 
   ARG   0.000   0.000   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 128}

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   1.46 %
                favored =  91.97 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   9.02
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.77
  MolProbity score      =   2.26

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  12" pdb=" CB  GLU A  75 "
  Number of C-beta restraints generated:  262

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Ramachandran outliers =   3.65 %
                favored =  79.56 %
  Rotamer outliers      =  21.77 %
  C-beta deviations     =     0
  Clashscore            =  18.94
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.53

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 105
        1.23 -     1.43: 368
        1.43 -     1.62: 659
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" C   ASP A  74 "
       model="  12" pdb=" N   GLU A  75 "
    ideal  model  delta    sigma   weight residual
    1.329  1.288  0.041 1.40e-02 5.10e+03 8.74e+00
  bond model="  12" pdb=" CZ  ARG A  21 "
       model="  12" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.63e+00
  bond model="  12" pdb=" CD2 HIS A 139 "
       model="  12" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.79e+00
  bond model="  12" pdb=" CD2 HIS A 138 "
       model="  12" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.65e+00
  bond model="  12" pdb=" CD2 HIS A 135 "
       model="  12" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.60e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       97.40 -   104.01: 28
      104.01 -   110.62: 2238
      110.62 -   117.23: 791
      117.23 -   123.85: 894
      123.85 -   130.46: 128
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" CA  GLU A  75 "
        model="  12" pdb=" C   GLU A  75 "
        model="  12" pdb=" O   GLU A  75 "
      ideal   model   delta    sigma   weight residual
     120.80  129.78   -8.98 1.70e+00 3.46e-01 2.79e+01
  angle model="  12" pdb=" CA  GLU A  75 "
        model="  12" pdb=" C   GLU A  75 "
        model="  12" pdb=" N   SER A  76 "
      ideal   model   delta    sigma   weight residual
     116.20  105.91   10.29 2.00e+00 2.50e-01 2.65e+01
  angle model="  12" pdb=" C   SER A  76 "
        model="  12" pdb=" N   ILE A  77 "
        model="  12" pdb=" CA  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     121.70  130.46   -8.76 1.80e+00 3.09e-01 2.37e+01
  angle model="  12" pdb=" C   GLY A  73 "
        model="  12" pdb=" N   ASP A  74 "
        model="  12" pdb=" CA  ASP A  74 "
      ideal   model   delta    sigma   weight residual
     121.70  113.33    8.37 1.80e+00 3.09e-01 2.16e+01
  angle model="  12" pdb=" OE1 GLN A  28 "
        model="  12" pdb=" CD  GLN A  28 "
        model="  12" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.25    4.35 1.00e+00 1.00e+00 1.89e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.30: 901
       16.30 -    32.60: 92
       32.60 -    48.90: 24
       48.90 -    65.19: 10
       65.19 -    81.49: 4
  Dihedral angle restraints: 1031
    sinusoidal: 562
      harmonic: 469
  Sorted by residual:
  dihedral model="  12" pdb=" CA  ASN A  72 "
           model="  12" pdb=" C   ASN A  72 "
           model="  12" pdb=" N   GLY A  73 "
           model="  12" pdb=" CA  GLY A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  107.74   72.26     0      5.00e+00 4.00e-02 2.09e+02
  dihedral model="  12" pdb=" CA  GLY A  73 "
           model="  12" pdb=" C   GLY A  73 "
           model="  12" pdb=" N   ASP A  74 "
           model="  12" pdb=" CA  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.71   52.29     0      5.00e+00 4.00e-02 1.09e+02
  dihedral model="  12" pdb=" CA  ASP A  74 "
           model="  12" pdb=" C   ASP A  74 "
           model="  12" pdb=" N   GLU A  75 "
           model="  12" pdb=" CA  GLU A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -129.77  -50.23     0      5.00e+00 4.00e-02 1.01e+02
  ... (remaining 1028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.876: 175
       0.876 -    1.752: 0
       1.752 -    2.629: 0
       2.629 -    3.505: 0
       3.505 -    4.381: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  GLU A  75 "
            model="  12" pdb=" N   GLU A  75 "
            model="  12" pdb=" C   GLU A  75 "
            model="  12" pdb=" CB  GLU A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.87    4.38 2.00e-01 2.50e+01 4.80e+02
  chirality model="  12" pdb=" CA  TYR A  81 "
            model="  12" pdb=" N   TYR A  81 "
            model="  12" pdb=" C   TYR A  81 "
            model="  12" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.05e+00
  chirality model="  12" pdb=" CA  ASP A 103 "
            model="  12" pdb=" N   ASP A 103 "
            model="  12" pdb=" C   ASP A 103 "
            model="  12" pdb=" CB  ASP A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.02e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  PHE A  67 "   -0.339 2.00e-02 2.50e+03   1.46e-01 6.36e+02
        model="  12" pdb=" CG  PHE A  67 "    0.004 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 PHE A  67 "    0.092 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 PHE A  67 "    0.065 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 PHE A  67 "    0.011 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 PHE A  67 "    0.036 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  PHE A  67 "   -0.083 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 PHE A  67 "    0.204 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 PHE A  67 "    0.123 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 PHE A  67 "    0.019 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 PHE A  67 "    0.097 2.00e-02 2.50e+03
        model="  12" pdb=" HZ  PHE A  67 "   -0.229 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  50 "   -0.299 2.00e-02 2.50e+03   1.17e-01 4.12e+02
        model="  12" pdb=" CG  TYR A  50 "    0.038 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  50 "    0.060 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  50 "    0.078 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  50 "   -0.079 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  50 "   -0.142 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  50 "    0.101 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  50 "    0.155 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  50 "    0.059 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  50 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  89 "   -0.232 2.00e-02 2.50e+03   9.88e-02 2.93e+02
        model="  12" pdb=" CG  TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  89 "    0.056 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  89 "    0.042 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  89 "    0.018 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  89 "    0.031 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  89 "   -0.044 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  89 "   -0.171 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  89 "    0.119 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  89 "    0.075 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  89 "    0.032 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  89 "    0.073 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.35: 601
        2.35 -     2.91: 5259
        2.91 -     3.47: 5430
        3.47 -     4.04: 7048
        4.04 -     4.60: 10415
  Nonbonded interactions: 28753
  Sorted by model distance:
  nonbonded model="  12" pdb=" OD2 ASP A  44 "
            model="  12" pdb=" HG  SER A  46 "
     model   vdw
     1.783 1.850
  nonbonded model="  12" pdb=" H   ILE A  86 "
            model="  12" pdb="HD12 ILE A  86 "
     model   vdw
     1.785 2.270
  nonbonded model="  12" pdb=" OE1 GLU A  24 "
            model="  12" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.800 1.850
  nonbonded model="  12" pdb="HG22 VAL A  41 "
            model="  12" pdb="HD12 ILE A 108 "
     model   vdw
     1.800 2.440
  nonbonded model="  12" pdb=" HA  GLU A  75 "
            model="  12" pdb=" H   SER A  76 "
     model   vdw
     1.812 2.270
  ... (remaining 28748 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.25, per 1000 atoms: 0.56
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.952, 51.411, 56.938, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.557)
  Mean delta:    0.001 (Z=  0.063)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.592 (Z=  1.354)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   88.317
  Mean delta:   23.811

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.095
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.046
    Angle     :  0.979   4.832   4077  Z= 0.341
    Chirality :  0.035   0.095    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.515  88.317    768
    Min Nonbonded Distance : 1.541
  
  Molprobity Statistics.
    All-atom Clashscore : 22.10
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  : 18.25 %
      Favored  : 75.91 %
    Rotamer:
      Outliers : 25.81 %
      Allowed  : 14.52 %
      Favored  : 59.68 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -7.02 (0.41), residues: 137
    helix: -4.28 (0.31), residues: 69
    sheet:  None (None), residues: 0
    loop : -5.22 (0.49), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 134 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.002   0.001   TYR A 105 
   ARG   0.001   0.000   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 134 
   PHE   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A  89 
   ARG   0.001   0.000   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  28  GLN
   A 137  HIS

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A LEU  119": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2216
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2216
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.10
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  LYS A  79 "
        model="   4" pdb=" CB  TYR A  89 "
        model="   4" pdb=" CB  THR A  92 "
        model="   4" pdb=" CB  LEU A  93 "
        model="   4" pdb=" CB  SER A  98 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Ramachandran outliers =   5.84 %
                favored =  75.91 %
  Rotamer outliers      =  25.81 %
  C-beta deviations     =     0
  Clashscore            =  22.10
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.70

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 58
        1.23 -     1.43: 416
        1.43 -     1.62: 651
        1.62 -     1.82: 11
  Bond restraints: 2242
  Sorted by residual:
  bond model="   4" pdb=" N   GLY A  80 "
       model="   4" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.686 -0.235 1.60e-02 3.91e+03 2.15e+02
  bond model="   4" pdb=" N   ILE A  77 "
       model="   4" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.713 -0.255 1.90e-02 2.77e+03 1.81e+02
  bond model="   4" pdb=" N   LYS A  79 "
       model="   4" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.667 -0.209 1.90e-02 2.77e+03 1.21e+02
  bond model="   4" pdb=" CA  ILE A  78 "
       model="   4" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.752 -0.227 2.10e-02 2.27e+03 1.17e+02
  bond model="   4" pdb=" CA  LYS A  79 "
       model="   4" pdb=" C   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.525  1.740 -0.215 2.10e-02 2.27e+03 1.05e+02
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       55.49 -    78.60: 3
       78.60 -   101.71: 36
      101.71 -   124.82: 3909
      124.82 -   147.93: 129
      147.93 -   171.04: 2
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CA  ILE A  78 "
        model="   4" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00  171.04  -62.04 3.00e+00 1.11e-01 4.28e+02
  angle model="   4" pdb=" CA  ILE A  77 "
        model="   4" pdb=" CB  ILE A  77 "
        model="   4" pdb=" CG2 ILE A  77 "
      ideal   model   delta    sigma   weight residual
     110.50  141.64  -31.14 1.70e+00 3.46e-01 3.36e+02
  angle model="   4" pdb=" C   ILE A  78 "
        model="   4" pdb=" CA  ILE A  78 "
        model="   4" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   55.49   53.51 3.00e+00 1.11e-01 3.18e+02
  angle model="   4" pdb=" C   ILE A  78 "
        model="   4" pdb=" N   LYS A  79 "
        model="   4" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  153.13  -31.43 1.80e+00 3.09e-01 3.05e+02
  angle model="   4" pdb=" C   LYS A  79 "
        model="   4" pdb=" N   GLY A  80 "
        model="   4" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  147.67  -25.97 1.80e+00 3.09e-01 2.08e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.80: 923
       22.80 -    45.61: 70
       45.61 -    68.41: 23
       68.41 -    91.22: 2
       91.22 -   114.02: 3
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   4" pdb=" C   ILE A  78 "
           model="   4" pdb=" N   ILE A  78 "
           model="   4" pdb=" CA  ILE A  78 "
           model="   4" pdb=" CB  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -179.42   57.42     0      2.50e+00 1.60e-01 5.28e+02
  dihedral model="   4" pdb=" CA  LYS A  79 "
           model="   4" pdb=" C   LYS A  79 "
           model="   4" pdb=" N   GLY A  80 "
           model="   4" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   65.98  114.02     0      5.00e+00 4.00e-02 5.20e+02
  dihedral model="   4" pdb=" N   ILE A  78 "
           model="   4" pdb=" C   ILE A  78 "
           model="   4" pdb=" CA  ILE A  78 "
           model="   4" pdb=" CB  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  179.41  -56.01     0      2.50e+00 1.60e-01 5.02e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.030: 165
       1.030 -    2.059: 2
       2.059 -    3.089: 1
       3.089 -    4.118: 2
       4.118 -    5.148: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CA  THR A  92 "
            model="   4" pdb=" N   THR A  92 "
            model="   4" pdb=" C   THR A  92 "
            model="   4" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.62    5.15 2.00e-01 2.50e+01 6.62e+02
  chirality model="   4" pdb=" CB  ILE A  78 "
            model="   4" pdb=" CA  ILE A  78 "
            model="   4" pdb=" CG1 ILE A  78 "
            model="   4" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.48    5.13 2.00e-01 2.50e+01 6.57e+02
  chirality model="   4" pdb=" CA  SER A  98 "
            model="   4" pdb=" N   SER A  98 "
            model="   4" pdb=" C   SER A  98 "
            model="   4" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.60    5.11 2.00e-01 2.50e+01 6.53e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  91 "    0.261 2.00e-02 2.50e+03   1.53e-01 7.03e+02
        model="   4" pdb=" CG  TYR A  91 "    0.020 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  91 "   -0.093 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  91 "   -0.005 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  91 "   -0.100 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  91 "    0.014 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  91 "    0.284 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  91 "   -0.229 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  91 "    0.040 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  91 "    0.046 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  91 "   -0.238 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A 105 "    0.164 2.00e-02 2.50e+03   7.05e-02 1.49e+02
        model="   4" pdb=" CG  TYR A 105 "   -0.017 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A 105 "   -0.027 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A 105 "   -0.042 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A 105 "   -0.029 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A 105 "   -0.015 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A 105 "    0.009 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A 105 "    0.136 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A 105 "   -0.032 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A 105 "   -0.077 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A 105 "   -0.056 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A 105 "   -0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  HIS A 136 "   -0.091 2.00e-02 2.50e+03   5.34e-02 5.71e+01
        model="   4" pdb=" CG  HIS A 136 "    0.072 2.00e-02 2.50e+03
        model="   4" pdb=" ND1 HIS A 136 "    0.073 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 HIS A 136 "    0.017 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 HIS A 136 "   -0.009 2.00e-02 2.50e+03
        model="   4" pdb=" NE2 HIS A 136 "   -0.041 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 HIS A 136 "    0.018 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 HIS A 136 "   -0.040 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     1.95: 46
        1.95 -     2.62: 2553
        2.62 -     3.28: 7049
        3.28 -     3.94: 8959
        3.94 -     4.60: 13100
  Nonbonded interactions: 31707
  Sorted by model distance:
  nonbonded model="   4" pdb=" HB  ILE A  77 "
            model="   4" pdb=" HA  LYS A  79 "
     model   vdw
     1.293 2.440
  nonbonded model="   4" pdb=" HA  ILE A  77 "
            model="   4" pdb=" HB  ILE A  77 "
     model   vdw
     1.369 1.952
  nonbonded model="   4" pdb=" H   ILE A  77 "
            model="   4" pdb=" HA  ILE A  78 "
     model   vdw
     1.470 2.270
  nonbonded model="   4" pdb=" HB3 ASP A  74 "
            model="   4" pdb=" H   LYS A  79 "
     model   vdw
     1.641 2.270
  nonbonded model="   4" pdb="HD12 LEU A  93 "
            model="   4" pdb=" H   GLY A  94 "
     model   vdw
     1.712 2.270
  ... (remaining 31702 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.23, per 1000 atoms: 0.55
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.537, 47.124, 42.454, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  89  TYR  N
   A  89  TYR  CA          1.46     1.56    -0.10  1.90e-02  2.67e+01   5.2*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.55    -0.09  1.90e-02  2.43e+01   4.9*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.61    -0.09  2.10e-02  1.71e+01   4.1*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.61    -0.08  2.10e-02  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.098 (Z=  5.164)
  Mean delta:    0.015 (Z=  0.795)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   150.20   -28.50  1.80e+00  2.51e+02  15.8*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   134.44   -23.44  2.80e+00  7.01e+01   8.4*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   110.19    12.81  1.60e+00  6.41e+01   8.0*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   127.39   -13.49  1.80e+00  5.62e+01   7.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.67   -10.77  1.50e+00  5.15e+01   7.2*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50    99.54    11.96  1.70e+00  4.95e+01   7.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   129.46   -13.26  2.00e+00  4.39e+01   6.6*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    93.02    17.98  2.80e+00  4.13e+01   6.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   133.19   -11.49  1.80e+00  4.07e+01   6.4*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   123.01   -13.91  2.20e+00  4.00e+01   6.3*sigma
   A 114  PRO  N
   A 114  PRO  CA
   A 114  PRO  C         112.10   126.92   -14.82  2.50e+00  3.51e+01   5.9*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   132.34   -10.64  1.80e+00  3.50e+01   5.9*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   123.33   -11.73  2.00e+00  3.44e+01   5.9*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.25   -10.65  2.00e+00  2.84e+01   5.3*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   119.25    -8.75  1.70e+00  2.65e+01   5.1*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   118.74    -8.34  1.70e+00  2.41e+01   4.9*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   122.53   -11.23  2.30e+00  2.38e+01   4.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.44    -4.84  1.00e+00  2.35e+01   4.8*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.43    -4.83  1.00e+00  2.33e+01   4.8*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  CB        110.50   118.54    -8.04  1.70e+00  2.24e+01   4.7*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   130.19    -8.49  1.80e+00  2.23e+01   4.7*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   118.87    -8.77  1.90e+00  2.13e+01   4.6*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   129.75    -8.05  1.80e+00  2.00e+01   4.5*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.59     5.61  1.30e+00  1.86e+01   4.3*sigma
   A  83  THR  CA
   A  83  THR  CB
   A  83  THR  CG2       110.50   117.84    -7.34  1.70e+00  1.86e+01   4.3*sigma
   A  92  THR  O
   A  92  THR  C
   A  93  LEU  N         123.00   116.12     6.88  1.60e+00  1.85e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.75e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30   101.08     8.22  2.00e+00  1.69e+01   4.1*sigma
   A  76  SER  C
   A  76  SER  CA
   A  76  SER  CB        110.10   117.80    -7.70  1.90e+00  1.64e+01   4.1*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O         120.80   127.68    -6.88  1.70e+00  1.64e+01   4.0*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N         116.20   108.17     8.03  2.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   28.501 (Z= 15.834)
  Mean delta:    2.626 (Z=  1.399)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00    50.54   129.46  5.00e+00  6.70e+02  25.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00    67.23   112.77  5.00e+00  5.09e+02  22.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   -93.48   -86.52  5.00e+00  2.99e+02  17.3*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   -99.19   -80.81  5.00e+00  2.61e+02  16.2*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   104.80    75.20  5.00e+00  2.26e+02  15.0*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   107.77    72.23  5.00e+00  2.09e+02  14.4*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   124.33    55.67  5.00e+00  1.24e+02  11.1*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   139.88    40.12  5.00e+00  6.44e+01   8.0*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   142.15    37.85  5.00e+00  5.73e+01   7.6*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   146.45    33.55  5.00e+00  4.50e+01   6.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   154.08    25.92  5.00e+00  2.69e+01   5.2*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -155.08   -24.92  5.00e+00  2.48e+01   5.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   158.65    21.35  5.00e+00  1.82e+01   4.3*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00  -159.10   -20.90  5.00e+00  1.75e+01   4.2*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -159.24   -20.76  5.00e+00  1.72e+01   4.2*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   159.29    20.71  5.00e+00  1.72e+01   4.1*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   159.47    20.53  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.010
  Max. delta:  129.462
  Mean delta:   18.096

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.42     5.94  2.00e-01  8.81e+02  29.7*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.59     5.23  2.00e-01  6.84e+02  26.2*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.61     5.16  2.00e-01  6.66e+02  25.8*sigma
   A  83  THR  CB
   A  83  THR  CA
   A  83  THR  OG1
   A  83  THR  CG2         2.55    -2.37     4.92  2.00e-01  6.06e+02  24.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.21     3.65  2.00e-01  3.32e+02  18.2*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     0.43     2.08  2.00e-01  1.08e+02  10.4*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43     1.28     1.15  2.00e-01  3.30e+01   5.7*sigma

  Min. delta:    0.001
  Max. delta:    5.935
  Mean delta:    0.878

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.161       0.280      516.00  14.0*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.061       0.115       75.47   5.7*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.049       0.086       47.92   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.161
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="LYS A  79  conformer  : H 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  78  ILE  HA , Angle CB-CA-HA, observed: 95.149, delta from target: 13.851
   A  51  ILE  HA , Angle C-CA-HA, observed: 94.349, delta from target: 14.651
   A  89  TYR  HA , Angle C-CA-HA, observed: 93.570, delta from target: 15.430
   A 114  PRO  HA , Angle CB-CA-HA, observed: 124.619, delta from target: -15.619
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.366, delta from target: 16.634
   A  78  ILE  HA , Angle C-CA-HA, observed: 90.430, delta from target: 18.570
   A  89  TYR  HA , Angle CB-CA-HA, observed: 148.272, delta from target: -39.272
   A  89  TYR  HA , Angle N-CA-HA, observed: 50.900, delta from target: 59.100

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.098   2241  Z= 0.566
    Angle     :  2.517  59.100   4077  Z= 1.074
    Chirality :  0.878   5.935    176
    Planarity :  0.014   0.163    326
    Dihedral  : 15.197 129.462    768
    Min Nonbonded Distance : 1.513
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  8.76 %
      Favored  : 86.86 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  4.84 %
      Favored  : 89.52 %
    Cbeta Deviations :  6.06 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 7.63 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.44 (0.64), residues: 137
    helix: -2.20 (0.46), residues: 78
    sheet:  None (None), residues: 0
    loop : -2.25 (0.84), residues: 59
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.095   0.015   PHE A  15 
   TYR   0.359   0.036   TYR A  91 
   ARG   0.008   0.002   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.066   0.015   PHE A  15 
   TYR   0.280   0.039   TYR A  91 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  10" pdb=" CB  LEU A   3 "
        model="  10" pdb=" CB  HIS A 134 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 0.60 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CB  ILE A  78 "
        model="   3" pdb=" CB  LYS A  79 "
        model="   3" pdb=" CB  THR A  92 "
        model="   3" pdb=" CB  LEU A  93 "
        model="   3" pdb=" CB  SER A  98 "
        model="   3" pdb=" CB  ASP A 116 "
        model="   3" pdb=" CB  ARG A 127 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   4.38 %
                favored =  86.86 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     8
  Clashscore            =   8.12
  RMS(bonds)            =   0.0108
  RMS(angles)           =   2.52
  MolProbity score      =   2.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2216
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 130}

============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 86
        1.23 -     1.42: 386
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.80e+00
  bond model="  10" pdb=" CD2 HIS A 139 "
       model="  10" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.77e+00
  bond model="  10" pdb=" CD2 HIS A 138 "
       model="  10" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.75e+00
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH1 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.323  1.288  0.035 1.40e-02 5.10e+03 6.18e+00
  bond model="  10" pdb=" CD2 HIS A 136 "
       model="  10" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.01e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       96.35 -   103.45: 19
      103.45 -   110.54: 2263
      110.54 -   117.64: 801
      117.64 -   124.74: 917
      124.74 -   131.84: 79
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  10" pdb=" C   LEU A   2 "
        model="  10" pdb=" N   LEU A   3 "
        model="  10" pdb=" CA  LEU A   3 "
      ideal   model   delta    sigma   weight residual
     121.70  131.84  -10.14 1.80e+00 3.09e-01 3.17e+01
  angle model="  10" pdb=" C   HIS A 134 "
        model="  10" pdb=" N   HIS A 135 "
        model="  10" pdb=" CA  HIS A 135 "
      ideal   model   delta    sigma   weight residual
     121.70  131.13   -9.43 1.80e+00 3.09e-01 2.75e+01
  angle model="  10" pdb=" C   GLU A 133 "
        model="  10" pdb=" N   HIS A 134 "
        model="  10" pdb=" CA  HIS A 134 "
      ideal   model   delta    sigma   weight residual
     121.70  130.67   -8.97 1.80e+00 3.09e-01 2.48e+01
  angle model="  10" pdb=" CA  HIS A 135 "
        model="  10" pdb=" CB  HIS A 135 "
        model="  10" pdb=" CG  HIS A 135 "
      ideal   model   delta    sigma   weight residual
     113.80  118.64   -4.84 1.00e+00 1.00e+00 2.35e+01
  angle model="  10" pdb=" CA  ASN A  72 "
        model="  10" pdb=" CB  ASN A  72 "
        model="  10" pdb=" CG  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     112.60  117.31   -4.71 1.00e+00 1.00e+00 2.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.98: 926
       16.98 -    33.96: 57
       33.96 -    50.94: 33
       50.94 -    67.92: 8
       67.92 -    84.90: 5
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  10" pdb=" CA  ILE A  51 "
           model="  10" pdb=" C   ILE A  51 "
           model="  10" pdb=" N   PRO A  52 "
           model="  10" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.59   31.41     0      5.00e+00 4.00e-02 3.95e+01
  dihedral model="  10" pdb=" CA  MET A 128 "
           model="  10" pdb=" C   MET A 128 "
           model="  10" pdb=" N   ARG A 129 "
           model="  10" pdb=" CA  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.47   22.53     0      5.00e+00 4.00e-02 2.03e+01
  dihedral model="  10" pdb=" CA  LEU A   3 "
           model="  10" pdb=" C   LEU A   3 "
           model="  10" pdb=" N   ILE A   4 "
           model="  10" pdb=" CA  ILE A   4 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.27   20.73     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.876: 174
       0.876 -    1.751: 0
       1.751 -    2.627: 0
       2.627 -    3.502: 0
       3Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

.502 -    4.378: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CA  HIS A 134 "
            model="  10" pdb=" N   HIS A 134 "
            model="  10" pdb=" C   HIS A 134 "
            model="  10" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.87    4.38 2.00e-01 2.50e+01 4.79e+02
  chirality model="  10" pdb=" CA  LEU A   3 "
            model="  10" pdb=" N   LEU A   3 "
            model="  10" pdb=" C   LEU A   3 "
            model="  10" pdb=" CB  LEU A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.85    4.36 2.00e-01 2.50e+01 4.75e+02
  chirality model="  10" pdb=" CA  HIS A 137 "
            model="  10" pdb=" N   HIS A 137 "
            model="  10" pdb=" C   HIS A 137 "
            model="  10" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  89 "   -0.186 2.00e-02 2.50e+03   1.06e-01 3.39e+02
        model="  10" pdb=" CG  TYR A  89 "   -0.025 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  89 "    0.060 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  89 "    0.058 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  89 "   -0.059 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  89 "   -0.187 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  89 "    0.155 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  89 "    0.175 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  12 "    0.173 2.00e-02 2.50e+03   7.84e-02 1.85e+02
        model="  10" pdb=" CG  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  12 "   -0.040 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  12 "   -0.030 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  12 "   -0.033 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  12 "    0.161 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  12 "   -0.078 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  12 "   -0.048 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  12 "   -0.033 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  12 "   -0.064 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  HIS A 134 "    0.150 2.00e-02 2.50e+03   9.24e-02 1.71e+02
        model="  10" pdb=" CG  HIS A 134 "   -0.119 2.00e-02 2.50e+03
        model="  10" pdb=" ND1 HIS A 134 "   -0.105 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 HIS A 134 "   -0.028 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 HIS A 134 "    0.016 2.00e-02 2.50e+03
        model="  10" pdb=" NE2 HIS A 134 "    0.124 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 HIS A 134 "   -0.062 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 HIS A 134 "    0.024 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 196
        2.23 -     2.82: 4503
        2.82 -     3.41: 5748
        3.41 -     4.01: 6963
        4.01 -     4.60: 10470
  Nonbonded interactions: 27880
  Sorted by model distance:
  nonbonded model="  10" pdb=" H   ILE A  86 "
            model="  10" pdb="HG13 ILE A  86 "
     model   vdw
     1.636 2.270
  nonbonded model="  10" pdb="HD21 LEU A  93 "
            model="  10" pdb=" H   ASP A 103 "
     model   vdw
     1.718 2.270
  nonbonded model="  10" pdb=" OE1 GLU A 123 "
            model="  10" pdb=" HZ2 LYS A 125 "
     model   vdw
     1.734 1.850
  nonbonded model="  10" pdb=" OE2 GLU A  16 "
            model="  10" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.782 1.850
  nonbonded model="  10" pdb=" OD1 ASP A  44 "
            model="  10" pdb=" HG  SER A  46 "
     model   vdw
     1.806 1.850
  ... (remaining 27875 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.562)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.601 (Z=  1.324)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   89.413
  Mean delta:   23.285

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.093
  Mean delta:    0.034

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.045
    Angle     :  0.979   4.826   4077  Z= 0.341
    Chirality :  0.034   0.093    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.455  89.413    768
    Min Nonbonded Distance : 1.710
  
  Molprobity Statistics.
    All-atom Clashscore : 22.10
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  : 16.06 %
      Favored  : 77.37 %
    Rotamer:
      Outliers : 20.16 %
      Allowed  : 24.19 %
      Favored  : 55.65 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -7.15 (0.39), residues: 137
    helix: -4.15 (0.33), residues: 66
    sheet:  None (None), residues: 0
    loop : -5.58 (0.43), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 134 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.002   0.001   TYR A  81 
   ARG   0.001   0.000   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 134 
   PHE   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A  81 
   ARG   0.001   0.000   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A 134  HIS

=================================== Summary ===================================

  Histogram of bond lengths:
        0.84 -     1.04: 1105
        1.04 -     1.23: 68
        1.23 -     1.43: 409
        1.43 -     1.62: 655
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   3" pdb=" C   THR A  92 "
       model="   3" pdb=" N   LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.262  0.067 1.40e-02 5.10e+03 2.31e+01
  bond model="   3" pdb=" N   ILE A  77 "
       model="   3" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.528 -0.070 1.90e-02 2.77e+03 1.36e+01
  bond model="   3" pdb=" CA  LYS A 125 "
       model="   3" pdb=" C   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.525  1.452  0.073 2.10e-02 2.27e+03 1.22e+01
  bond model="   3" pdb=" N   TYR A  91 "
       model="   3" pdb=" CA  TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.458  1.518 -0.060 1.90e-02 2.77e+03 9.97e+00
  bond model="   3" pdb=" N   GLY A  80 "
       model="   3" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.500 -0.049 1.60e-02 3.91e+03 9.49e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       89.14 -    99.42: 15
       99.42 -   109.70: 2027
      109.70 -   119.98: 1315
      119.98 -   130.26: 712
      130.26 -   140.53: 8
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   3" pdb=" C   SER A  90 "
        model="   3" pdb=" N   TYR A  91 "
        model="   3" pdb=" CA  TYR A  91 "
      ideal   model   delta    sigma   weight residual
     121.70  140.53  -18.83 1.80e+00 3.09e-01 1.09e+02
  angle model="   3" pdb=" C   THR A  92 "
        model="   3" pdb=" N   LEU A  93 "
        model="   3" pdb=" CA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     121.70  138.67  -16.97 1.80e+00 3.09e-01 8.88e+01
  angle model="   3" pdb=" N   LEU A  93 "
        model="   3" pdb=" CA  LEU A  93 "
        model="   3" pdb=" CB  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.50   95.45   15.05 1.70e+00 3.46e-01 7.84e+01
  angle model="   3" pdb=" C   LEU A  99 "
        model="   3" pdb=" CA  LEU A  99 "
        model="   3" pdb=" CB  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     110.10  124.16  -14.06 1.90e+00 2.77e-01 5.48e+01
  angle model="   3" pdb=" CA  THR A  92 "
        model="   3" pdb=" C   THR A  92 "
        model="   3" pdb=" N   LEU A  93 "
      ideal   model   delta    sigma   weight residual
     116.20  101.67   14.53 2.00e+00 2.50e-01 5.28e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.01: 939
       24.01 -    48.03: 55
       48.03 -    72.04: 18
       72.04 -    96.05: 1
       96.05 -   120.07: 3
  Dihedral angle restraints: 1016
    sinusoidal: 561
      harmonic: 455
  Sorted by residual:
  dihedral model="   3" pdb=" CA  SER A  90 "
           model="   3" pdb=" C   SER A  90 "
           model="   3" pdb=" N   TYR A  91 "
           model="   3" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   59.93  120.07     0      5.00e+00 4.00e-02 5.77e+02
  dihedral model="   3" pdb=" CA  ILE A 122 "
           model="   3" pdb=" C   ILE A 122 "
           model="   3" pdb=" N   GLU A 123 "
           model="   3" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   78.61  101.39     0      5.00e+00 4.00e-02 4.11e+02
  dihedral model="   3" pdb=" CA  VAL A 126 "
           model="   3" pdb=" C   VAL A 126 "
           model="   3" pdb=" N   ARG A 127 "
           model="   3" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   83.79   96.21     0      5.00e+00 4.00e-02 3.70e+02
  ... (remaining 1013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.003 -    1.141: 166
       1.141 -    2.279: 1
       2.279 -    3.417: 0
       3.417 -    4.556: 1
       4.556 -    5.694: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   3" pdb=" CA  LYS A  79 "
            model="   3" pdb=" N   LYS A  79 "
            model="   3" pdb=" C   LYS A  79 "
            model="   3" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.18    5.69 2.00e-01 2.50e+01 8.10e+02
  chirality model="   3" pdb=" CA  LEU A  93 "
            model="   3" pdb=" N   LEU A  93 "
            model="   3" pdb=" C   LEU A  93 "
            model="   3" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.83    5.34 2.00e-01 2.50e+01 7.13e+02
  chirality model="   3" pdb=" CA  ARG A 127 "
            model="   3" pdb=" N   ARG A 127 "
            model="   3" pdb=" C   ARG A 127 "
            model="   3" pdb=" CB  ARG A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.81    5.32 2.00e-01 2.50e+01 7.08e+02
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  91 "    0.402 2.00e-02 2.50e+03   2.03e-01 1.23e+03
        model="   3" pdb=" CG  TYR A  91 "    0.014 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  91 "   -0.069 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  91 "   -0.079 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  91 "   -0.095 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  91 "   -0.074 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  91 "    0.045 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  91 "    0.457 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  91 "   -0.108 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  91 "   -0.142 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  91 "   -0.202 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  91 "   -0.149 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  PHE A  67 "    0.190 2.00e-02 2.50e+03   8.09e-02 1.96e+02
        model="   3" pdb=" CG  PHE A  67 "    0.016 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 PHE A  67 "   -0.038 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 PHE A  67 "   -0.054 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 PHE A  67 "   -0.010 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 PHE A  67 "    0.006 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  PHE A  67 "    0.035 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 PHE A  67 "   -0.093 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 PHE A  67 "   -0.141 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 PHE A  67 "   -0.021 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 PHE A  67 "    0.026 2.00e-02 2.50e+03
        model="   3" pdb=" HZ  PHE A  67 "    0.084 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  89 "    0.166 2.00e-02 2.50e+03   6.90e-02 1.43e+02
        model="   3" pdb=" CG  TYR A  89 "    0.004 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  89 "   -0.028 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  89 "   -0.049 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  89 "    0.004 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  89 "    0.017 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  89 "    0.080 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  89 "   -0.056 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  89 "   -0.119 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  89 "   -0.033 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  89 "    0.031 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 229
        2.22 -     2.82: 4560
        2.82 -     3.41: 6368
        3.41 -     4.01: 7727
        4.01 -     4.60: 11644
  Nonbonded interactions: 30528
  Sorted by model distance:
  nonbonded model="   3" pdb="HD11 ILE A  77 "
            model="   3" pdb=" HB2 TYR A  91 "
     model   vdw
     1.628 2.440
  nonbonded model="   3" pdb=" H   TYR A  91 "
            model="   3" pdb="HG22 THR A  92 "
     model   vdw
     1.707 2.270
  nonbonded model="   3" pdb=" HA  ILE A  77 "
            model="   3" pdb=" H   LYS A  79 "
     model   vdw
     1.709 2.270
  nonbonded model="   3" pdb=" OD1 ASP A  44 "
            model="   3" pdb=" HG  SER A  46 "
     model   vdw
     1.815 1.850
  nonbonded model="   3" pdb=" OD2 ASP A  36 "
            model="   3" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.836 1.850
  ... (remaining 30523 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   6.57 %
                favored =  77.37 %
  Rotamer outliers      =  20.16 %
  C-beta deviations     =     0
  Clashscore            =  22.10
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.60

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 77
        1.23 -     1.42: 395
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" CZ  ARG A  21 "
       model="  13" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.58e+00
  bond model="  13" pdb=" CD2 HIS A 139 "
       model="  13" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.56e+00
  bond model="  13" pdb=" CD2 HIS A 136 "
       model="  13" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.55e+00
  bond model="  13" pdb=" CD2 HIS A 138 "
       model="  13" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.49e+00
  bond model="  13" pdb=" CD2 HIS A 135 "
       model="  13" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.37e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   106.23: 136
      106.23 -   111.92: 2468
      111.92 -   117.61: 478
      117.61 -   123.31: 816
      123.31 -   129.00: 181
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" CA  ASP A 103 "
        model="  13" pdb=" CB  ASP A 103 "
        model="  13" pdb=" CG  ASP A 103 "
      ideal   model   delta    sigma   weight residual
     112.60  108.09    4.51 1.00e+00 1.00e+00 2.04e+01
  angle model="  13" pdb=" OE1 GLN A  28 "
        model="  13" pdb=" CD  GLN A  28 "
        model="  13" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.29    4.31 1.00e+00 1.00e+00 1.86e+01
  angle model="  13" pdb=" OE1 GLN A 100 "
        model="  13" pdb=" CD  GLN A 100 "
        model="  13" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.29    4.31 1.00e+00 1.00e+00 1.86e+01
  angle model="  13" pdb=" CB  HIS A  43 "
        model="  13" pdb=" CG  HIS A  43 "
        model="  13" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  125.67    5.53 1.30e+00 5.92e-01 1.81e+01
  angle model="  13" pdb=" CD  ARG A  21 "
        model="  13" pdb=" NE  ARG A  21 "
        model="  13" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.00   -4.60 1.40e+00 5.10e-01 1.08e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.58: 900
       16.58 -    33.17: 85
       33.17 -    49.75: 33
       49.75 -    66.34: 8
       66.34 -    82.92: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  13" pdb=" CA  HIS A 137 "
           model="  13" pdb=" C   HIS A 137 "
           model="  13" pdb=" N   HIS A 138 "
           model="  13" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.78   22.22     0      5.00e+00 4.00e-02 1.98e+01
  dihedral model="  13" pdb=" C   ILE A  71 "
           model="  13" pdb=" N   ILE A  71 "
           model="  13" pdb=" CA  ILE A  71 "
           model="  13" pdb=" CB  ILE A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.38   10.38     0      2.50e+00 1.60e-01 1.72e+01
  dihedral model="  13" pdb=" N   ILE A  71 "
           model="  13" pdb=" C   ILE A  71 "
           model="  13" pdb=" CA  ILE A  71 "
           model="  13" pdb=" CB  ILE A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  132.81   -9.41     0      2.50e+00 1.60e-01 1.42e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 78
       0.053 -    0.107: 49
       0.107 -    0.160: 42
       0.160 -    0.214: 4
       0.214 -    0.267: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  ILE A  71 "
            model="  13" pdb=" N   ILE A  71 "
            model="  13" pdb=" C   ILE A  71 "
            model="  13" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.17    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality model="  13" pdb=" CG  LEU A  59 "
            model="  13" pdb=" CB  LEU A  59 "
            model="  13" pdb=" CD1 LEU A  59 "
            model="  13" pdb=" CD2 LEU A  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.83    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality model="  13" pdb=" CB  VAL A  14 "
            model="  13" pdb=" CA  VAL A  14 "
            model="  13" pdb=" CG1 VAL A  14 "
            model="  13" pdb=" CG2 VAL A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  81 "    0.153 2.00e-02 2.50e+03   7.15e-02 1.53e+02
        model="  13" pdb=" CG  TYR A  81 "    0.008 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  81 "   -0.032 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  81 "   -0.028 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  81 "   -0.028 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  81 "    0.012 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  81 "    0.152 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  81 "   -0.062 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  81 "   -0.051 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  81 "   -0.045 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  81 "   -0.055 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  HIS A  43 "    0.126 2.00e-02 2.50e+03   7.42e-02 1.10e+02
        model="  13" pdb=" CG  HIS A  43 "   -0.099 2.00e-02 2.50e+03
        model="  13" pdb=" ND1 HIS A  43 "   -0.106 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 HIS A  43 "   -0.023 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 HIS A  43 "    0.012 2.00e-02 2.50e+03
        model="  13" pdb=" NE2 HIS A  43 "    0.049 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 HIS A  43 "   -0.020 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 HIS A  43 "    0.061 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  12 "    0.107 2.00e-02 2.50e+03   5.84e-02 1.02e+02
        model="  13" pdb=" CG  TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  12 "   -0.050 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  12 "    0.027 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  12 "   -0.123 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  12 "   -0.042 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  12 "    0.092 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.39: 842
        2.39 -     2.94: 4953
        2.94 -     3.49: 5116
        3.49 -     4.05: 6562
        4.05 -     4.60: 9548
  Nonbonded interactions: 27021
  Sorted by model distance:
  nonbonded model="  13" pdb=" HZ2 LYS A  10 "
            model="  13" pdb=" OD1 ASP A  23 "
     model   vdw
     1.835 1.850
  nonbonded model="  13" pdb=" O   ILE A  30 "
            model="  13" pdb=" HG1 THR A  34 "
     model   vdw
     1.852 1.850
  nonbonded model="  13" pdb=" HE  ARG A  21 "
            model="  13" pdb=" HB3 LEU A  25 "
     model   vdw
     1.880 2.270
  nonbonded model="  13" pdb=" HH  TYR A  91 "
            model="  13" pdb=" O   LEU A 107 "
     model   vdw
     1.894 1.850
  nonbonded model="  13" pdb="HG12 ILE A  38 "
            model="  13" pdb=" H   PHE A  45 "
     model   vdw
     1.913 2.270
  ... (remaining 27016 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2216
  At special positions: 0
  Unit cell: (45.698, 42.587, 51.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1104      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 0.86, per 1000 atoms: 0.39
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (71.149, 66.567, 48.937, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A LEU    2": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2202
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 1.12, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (66.587, 47.491, 56.927, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.524, 51.696, 53.801, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   70": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A LEU  119": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   6"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  14"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.06, per 1000 atoms: 0.48
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (38.326, 66.071, 62.588, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.574, 52.325, 58.052, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  MET A   1 "
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  ILE A  78 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CB  SER A  90 "
        model="   1" pdb=" CB  THR A  92 "
        model="   1" pdb=" CB  GLU A 123 "
        model="   1" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.29 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 95
        1.23 -     1.43: 380
        1.43 -     1.63: 657
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   1" pdb=" N   GLY A  80 "
       model="   1" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.570 -0.119 1.60e-02 3.91e+03 5.57e+01
  bond model="   1" pdb=" N   ILE A  77 "
       model="   1" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.554 -0.096 1.90e-02 2.77e+03 2.56e+01
  bond model="   1" pdb=" CA  ASP A  88 "
       model="   1" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.625 -0.100 2.10e-02 2.27e+03 2.28e+01
  bond model="   1" pdb=" N   TYR A  89 "
       model="   1" pdb=" CA  TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.547 -0.089 1.90e-02 2.77e+03 2.19e+01
  bond model="   1" pdb=" CB  THR A  92 "
       model="   1" pdb=" OG1 THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.433  1.380  0.053 1.60e-02 3.91e+03 1.11e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       90.38 -   101.27: 20
      101.27 -   112.16: 2545
      112.16 -   123.05: 1262
      123.05 -   133.94: 250
      133.94 -   144.83: 2
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   1" pdb=" C   ILE A  78 "
        model="   1" pdb=" N   LYS A  79 "
        model="   1" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  144.83  -23.13 1.80e+00 3.09e-01 1.65e+02
  angle model="   1" pdb=" CA  THR A  92 "
        model="   1" pdb=" CB  THR A  92 "
        model="   1" pdb=" CG2 THR A  92 "
      ideal   model   delta    sigma   weight residual
     110.50  126.03  -15.53 1.70e+00 3.46e-01 8.35e+01
  angle model="   1" pdb=" C   LYS A  79 "
        model="   1" pdb=" N   GLY A  80 "
        model="   1" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  137.20  -15.50 1.80e+00 3.09e-01 7.41e+01
  angle model="   1" pdb=" C   ASP A  74 "
        model="   1" pdb=" CA  ASP A  74 "
        model="   1" pdb=" CB  ASP A  74 "
      ideal   model   delta    sigma   weight residual
     110.10  125.25  -15.15 1.90e+00 2.77e-01 6.35e+01
  angle model="   1" pdb=" C   ILE A  78 "
        model="   1" pdb=" CA  ILE A  78 "
        model="   1" pdb=" CB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     111.60  126.76  -15.16 2.00e+00 2.50e-01 5.75e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.77: 930
       18.77 -    37.54: 57
       37.54 -    56.31: 23
       56.31 -    75.08: 4
       75.08 -    93.85: 3
  Dihedral angle restraints: 1017
    sinusoidal: 562
      harmonic: 455
  Sorted by residual:
  dihedral model="   1" pdb=" CA  ILE A 122 "
           model="   1" pdb=" C   ILE A 122 "
           model="   1" pdb=" N   GLU A 123 "
           model="   1" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   86.15   93.85     0      5.00e+00 4.00e-02 3.52e+02
  dihedral model="   1" pdb=" CA  LYS A  79 "
           model="   1" pdb=" C   LYS A  79 "
           model="   1" pdb=" N   GLY A  80 "
           model="   1" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   97.30   82.70     0      5.00e+00 4.00e-02 2.74e+02
  dihedral model="   1" pdb=" CA  SER A  90 "
           model="   1" pdb=" C   SER A  90 "
           model="   1" pdb=" N   TYR A  91 "
           model="   1" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -98.86  -81.14     0      5.00e+00 4.00e-02 2.63e+02
  ... (remaining 1014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    1.122: 166
       1.122 -    2.243: 0
       2.243 -    3.363: 0
       3.363 -    4.484: 3
       4.484 -    5.604: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  LYS A  79 "
            model="   1" pdb=" N   LYS A  79 "
            model="   1" pdb=" C   LYS A  79 "
            model="   1" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.09    5.60 2.00e-01 2.50e+01 7.85e+02
  chirality model="   1" pdb=" CB  ILE A  78 "
            model="   1" pdb=" CA  ILE A  78 "
            model="   1" pdb=" CG1 ILE A  78 "
            model="   1" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.67    5.32 2.00e-01 2.50e+01 7.07e+02
  chirality model="   1" pdb=" CA  THR A  92 "
            model="   1" pdb=" N   THR A  92 "
            model="   1" pdb=" C   THR A  92 "
            model="   1" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.72    5.24 2.00e-01 2.50e+01 6.87e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  50 "   -0.172 2.00e-02 2.50e+03   7.30e-02 1.60e+02
        model="   1" pdb=" CG  TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  50 "    0.035 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  50 "    0.037 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  50 "   -0.145 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  50 "    0.053 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  50 "    0.059 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  50 "    0.040 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  50 "    0.034 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  HIS A 137 "    0.135 2.00e-02 2.50e+03   8.02e-02 1.29e+02
        model="   1" pdb=" CG  HIS A 137 "   -0.114 2.00e-02 2.50e+03
        model="   1" pdb=" ND1 HIS A 137 "   -0.111 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 HIS A 137 "   -0.025 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 HIS A 137 "    0.013 2.00e-02 2.50e+03
        model="   1" pdb=" NE2 HIS A 137 "    0.044 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 HIS A 137 "   -0.013 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 HIS A 137 "    0.070 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  89 "    0.006 2.00e-02 2.50e+03   5.24e-02 8.25e+01
        model="   1" pdb=" CG  TYR A  89 "    0.063 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  89 "    0.025 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  89 "   -0.011 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  89 "   -0.037 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  89 "    0.018 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  89 "    0.082 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  89 "    0.042 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  89 "   -0.068 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  89 "   -0.116 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  89 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     1.96: 43
        1.96 -     2.62: 2616
        2.62 -     3.28: 7105
        3.28 -     3.94: 8710
        3.94 -     4.60: 13196
  Nonbonded interactions: 31670
  Sorted by model distance:
  nonbonded model="   1" pdb=" HA  ILE A  77 "
            model="   1" pdb=" H   LYS A  79 "
     model   vdw
     1.301 2.270
  nonbonded model="   1" pdb=" H   LEU A  93 "
            model="   1" pdb=" H   GLY A  94 "
     model   vdw
     1.660 2.100
  nonbonded model="   1" pdb=" HA  TYR A  89 "
            model="   1" pdb=" HA  SER A  90 "
     model   vdw
     1.713 2.440
  nonbonded model="   1" pdb=" OD2 ASP A  74 "
            model="   1" pdb=" HH  TYR A  91 "
     model   vdw
     1.760 1.850
  nonbonded model="   1" pdb=" OD1 ASP A  44 "
            model="   1" pdb=" HG  SER A  46 "
     model   vdw
     1.788 1.850
  ... (remaining 31665 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 3, 'PTRANS': 7, 'TRANS': 128}
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.004, 58.092, 46.654, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2202
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
          Chain breaks: 1

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  13"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  11"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (65.539, 41.701, 54.287, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 79
        1.23 -     1.42: 393
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" CD2 HIS A 139 "
       model="  14" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.406 -0.032 1.10e-02 8.26e+03 8.62e+00
  bond model="  14" pdb=" CE1 HIS A  43 "
       model="  14" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.72e+00
  bond model="  14" pdb=" CE1 HIS A 136 "
       model="  14" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.04e+00
  bond model="  14" pdb=" CZ  ARG A  58 "
       model="  14" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.95e+00
  bond model="  14" pdb=" CD2 HIS A 134 "
       model="  14" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.90e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.48 -   105.43: 75
      105.43 -   111.39: 2380
      111.39 -   117.34: 594
      117.34 -   123.29: 842
      123.29 -   129.25: 188
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" CG1 VAL A 112 "
        model="  14" pdb=" CB  VAL A 112 "
        model="  14" pdb=" CG2 VAL A 112 "
      ideal   model   delta    sigma   weight residual
     110.80   99.48   11.32 2.20e+00 2.07e-01 2.65e+01
  angle model="  14" pdb=" OE1 GLN A  66 "
        model="  14" pdb=" CD  GLN A  66 "
        model="  14" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.81    4.79 1.00e+00 1.00e+00 2.29e+01
  angle model="  14" pdb=" CA  VAL A 112 "
        model="  14" pdb=" CB  VAL A 112 "
        model="  14" pdb=" CG1 VAL A 112 "
      ideal   model   delta    sigma   weight residual
     110.40  118.05   -7.65 1.70e+00 3.46e-01 2.03e+01
  angle model="  14" pdb=" CA  HIS A 139 "
        model="  14" pdb=" CB  HIS A 139 "
        model="  14" pdb=" CG  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     113.80  118.08   -4.28 1.00e+00 1.00e+00 1.83e+01
  angle model="  14" pdb=" CB  HIS A 138 "
        model="  14" pdb=" CG  HIS A 138 "
        model="  14" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  125.79    5.41 1.30e+00 5.92e-01 1.73e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 931
       17.56 -    35.13: 67
       35.13 -    52.69: 20
       52.69 -    70.25: 7
       70.25 -    87.82: 8
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  14" pdb=" C   ILE A 108 "
           model="  14" pdb=" N   ILE A 108 "
           model="  14" pdb=" CA  ILE A 108 "
           model="  14" pdb=" CB  ILE A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.22   13.22     0      2.50e+00 1.60e-01 2.80e+01
  dihedral model="  14" pdb=" CA  LYS A 113 "
           model="  14" pdb=" C   LYS A 113 "
           model="  14" pdb=" N   PRO A 114 "
           model="  14" pdb=" CA  PRO A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.64   22.36     0      5.00e+00 4.00e-02 2.00e+01
  dihedral model="  14" pdb=" N   ILE A 108 "
           model="  14" pdb=" C   ILE A 108 "
           model="  14" pdb=" CA  ILE A 108 "
           model="  14" pdb=" CB  ILE A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  132.86   -9.46     0      2.50e+00 1.60e-01 1.43e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 90
       0.062 -    0.123: 58
       0.123 -    0.185: 22
       0.185 -    0.247: 5
       0.247 -    0.308: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CA  ILE A 108 "
            model="  14" pdb=" N   ILE A 108 "
            model="  14" pdb=" C   ILE A 108 "
            model="  14" pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.13    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality model="  14" pdb=" CA  ARG A 129 "
            model="  14" pdb=" N   ARG A 129 "
            model="  14" pdb=" C   ARG A 129 "
            model="  14" pdb=" CB  ARG A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality model="  14" pdb=" CG  LEU A  53 "
            model="  14" pdb=" CB  LEU A  53 "
            model="  14" pdb=" CD1 LEU A  53 "
            model="  14" pdb=" CD2 LEU A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.83    0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  91 "   -0.160 2.00e-02 2.50e+03   1.04e-01 3.27e+02
        model="  14" pdb=" CG  TYR A  91 "   -0.027 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  91 "    0.053 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  91 "    0.066 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  91 "    0.011 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  91 "   -0.036 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  91 "   -0.211 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  91 "   -0.027 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  91 "    0.134 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  91 "    0.181 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  91 "    0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  89 "    0.064 2.00e-02 2.50e+03   9.73e-02 2.84e+02
        model="  14" pdb=" CG  TYR A  89 "   -0.024 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  89 "   -0.071 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  89 "    0.029 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  89 "    0.063 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  89 "   -0.036 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  89 "   -0.034 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  89 "   -0.190 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  89 "    0.106 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  89 "    0.199 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  89 "   -0.099 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  50 "    0.195 2.00e-02 2.50e+03   8.45e-02 2.14e+02
        model="  14" pdb=" CG  TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  50 "   -0.034 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  50 "   -0.047 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  50 "   -0.034 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  50 "    0.171 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  50 "   -0.048 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  50 "   -0.085 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  50 "   -0.058 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  50 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.31: 425
        2.31 -     2.89: 5027
        2.89 -     3.46: 5470
        3.46 -     4.03: 7109
        4.03 -     4.60: 10574
  Nonbonded interactions: 28605
  Sorted by model distance:
  nonbonded model="  14" pdb=" OE1 GLU A  75 "
            model="  14" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.744 1.850
  nonbonded model="  14" pdb=" HG  SER A  17 "
            model="  14" pdb=" OD2 ASP A  74 "
     model   vdw
     1.782 1.850
  nonbonded model="  14" pdb=" OE2 GLU A  16 "
            model="  14" pdb=" HZ1 LYS A  19 "
     model   vdw
     1.834 1.850
  nonbonded model="  14" pdb=" HZ3 LYS A  10 "
            model="  14" pdb=" OD1 ASP A  23 "
     model   vdw
     1.837 1.850
  nonbonded model="  14" pdb=" OE1 GLU A  49 "
            model="  14" pdb=" HH  TYR A  50 "
     model   vdw
     1.868 1.850
  ... (remaining 28600 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.20, per 1000 atoms: 0.54
  Number of scatterers: 2202
  At special positions: 0
  Unit cell: (51.61, 66.65, 49.753, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1090      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 0.76, per 1000 atoms: 0.34
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.196, 40.204, 56.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 1.12, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (54.65, 53.891, 59.045, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

  Time building chain proxies: 0.85, per 1000 atoms: 0.38
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.23, 80.212, 45.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.164, 41.783, 49.984, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.06 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (42.573, 57.627, 53.734, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 60
        1.23 -     1.42: 412
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" CZ  ARG A  21 "
       model="  13" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.23e+00
  bond model="  13" pdb=" CD2 HIS A 138 "
       model="  13" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.21e+00
  bond model="  13" pdb=" CD2 HIS A 134 "
       model="  13" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.60e+00
  bond model="  13" pdb=" CE1 HIS A 139 "
       model="  13" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.48e+00
  bond model="  13" pdb=" CD2 HIS A 136 "
       model="  13" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.43e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.39 -   105.31: 64
      105.31 -   111.22: 2393
      111.22 -   117.14: 594
      117.14 -   123.06: 797
      123.06 -   128.98: 231
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" OE1 GLN A  28 "
        model="  13" pdb=" CD  GLN A  28 "
        model="  13" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.25    4.35 1.00e+00 1.00e+00 1.89e+01
  angle model="  13" pdb=" OE1 GLN A 100 "
        model="  13" pdb=" CD  GLN A 100 "
        model="  13" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.54    4.06 1.00e+00 1.00e+00 1.65e+01
  angle model="  13" pdb=" OE1 GLN A  66 "
        model="  13" pdb=" CD  GLN A  66 "
        model="  13" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.55    4.05 1.00e+00 1.00e+00 1.64e+01
  angle model="  13" pdb=" CA  ASP A 103 "
        model="  13" pdb=" CB  ASP A 103 "
        model="  13" pdb=" CG  ASP A 103 "
      ideal   model   delta    sigma   weight residual
     112.60  108.82    3.78 1.00e+00 1.00e+00 1.43e+01
  angle model="  13" pdb=" CD  ARG A  21 "
        model="  13" pdb=" NE  ARG A  21 "
        model="  13" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.98   -4.58 1.40e+00 5.10e-01 1.07e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.39: 909
       16.39 -    32.78: 81
       32.78 -    49.18: 24
       49.18 -    65.57: 12
       65.57 -    81.96: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  13" pdb=" CA  LYS A  85 "
           model="  13" pdb=" C   LYS A  85 "
           model="  13" pdb=" N   ILE A  86 "
           model="  13" pdb=" CA  ILE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.37   27.63     0      5.00e+00 4.00e-02 3.05e+01
  dihedral model="  13" pdb=" CA  GLU A 133 "
           model="  13" pdb=" C   GLU A 133 "
           model="  13" pdb=" N   HIS A 134 "
           model="  13" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.97  -25.03     0      5.00e+00 4.00e-02 2.51e+01
  dihedral model="  13" pdb=" CA  ILE A  51 "
           model="  13" pdb=" C   ILE A  51 "
           model="  13" pdb=" N   PRO A  52 "
           model="  13" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   24.79  -24.79     0      5.00e+00 4.00e-02 2.46e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 81
       0.057 -    0.113: 55
       0.113 -    0.170: 31
       0.170 -    0.226: 6
       0.226 -    0.283: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  LYS A  79 "
            model="  13" pdb=" N   LYS A  79 "
            model="  13" pdb=" C   LYS A  79 "
            model="  13" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality model="  13" pdb=" CA  ARG A 127 "
            model="  13" pdb=" N   ARG A 127 "
            model="  13" pdb=" C   ARG A 127 "
            model="  13" pdb=" CB  ARG A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality model="  13" pdb=" CG  LEU A  70 "
            model="  13" pdb=" CB  LEU A  70 "
            model="  13" pdb=" CD1 LEU A  70 "
            model="  13" pdb=" CD2 LEU A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  89 "   -0.267 2.00e-02 2.50e+03   1.16e-01 4.01e+02
        model="  13" pdb=" CG  TYR A  89 "    0.016 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  89 "    0.077 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  89 "    0.038 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  89 "    0.015 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  89 "    0.051 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  89 "   -0.003 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  89 "   -0.208 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  89 "    0.157 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  89 "    0.044 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  89 "   -0.016 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  89 "    0.095 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  PHE A  15 "   -0.156 2.00e-02 2.50e+03   6.49e-02 1.27e+02
        model="  13" pdb=" CG  PHE A  15 "    0.013 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 PHE A  15 "    0.037 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 PHE A  15 "    0.037 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 PHE A  15 "    0.011 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 PHE A  15 "    0.010 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  PHE A  15 "   -0.038 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 PHE A  15 "    0.069 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 PHE A  15 "    0.071 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 PHE A  15 "    0.026 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 PHE A  15 "    0.024 2.00e-02 2.50e+03
        model="  13" pdb=" HZ  PHE A  15 "   -0.103 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  12 "   -0.131 2.00e-02 2.50e+03   6.00e-02 1.08e+02
        model="  13" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  12 "    0.028 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  12 "   -0.127 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  12 "    0.042 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  12 "    0.054 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  12 "    0.043 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  12 "    0.032 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 395
        2.32 -     2.89: 5026
        2.89 -     3.46: 5039
        3.46 -     4.03: 6324
        4.03 -     4.60: 9458
  Nonbonded interactions: 26242
  Sorted by model distance:
  nonbonded model="  13" pdb=" OD1 ASP A  44 "
            model="  13" pdb=" HG  SER A  46 "
     model   vdw
     1.751 1.850
  nonbonded model="  13" pdb=" OE2 GLU A  24 "
            model="  13" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.792 1.850
  nonbonded model="  13" pdb=" OE2 GLU A 123 "
            model="  13" pdb=" HZ2 LYS A 125 "
     model   vdw
     1.792 1.850
  nonbonded model="  13" pdb=" HZ1 LYS A  40 "
            model="  13" pdb=" OD2 ASP A 103 "
     model   vdw
     1.809 1.850
  nonbonded model="  13" pdb=" HZ1 LYS A  10 "
            model="  13" pdb=" OD1 ASP A  23 "
     model   vdw
     1.811 1.850
  ... (remaining 26237 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.13
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   0" pdb=" CB  ILE A  51 "
        model="   0" pdb=" CB  ILE A  78 "
        model="   0" pdb=" CB  LYS A  79 "
        model="   0" pdb=" CB  TYR A  89 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 1.28 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.71 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.55
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.67 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1104
        1.03 -     1.23: 58
        1.23 -     1.43: 417
        1.43 -     1.62: 657
        1.62 -     1.82: 4
  Bond restraints: 2240
  Sorted by residual:
  bond model="   0" pdb=" N   LYS A  79 "
       model="   0" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.592 -0.134 1.90e-02 2.77e+03 4.94e+01
  bond model="   0" pdb=" N   LEU A  93 "
       model="   0" pdb=" CA  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.458  1.356  0.102 1.90e-02 2.77e+03 2.87e+01
  bond model="   0" pdb=" N   TYR A  91 "
       model="   0" pdb=" CA  TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.458  1.538 -0.080 1.90e-02 2.77e+03 1.77e+01
  bond model="   0" pdb=" C   SER A  90 "
       model="   0" pdb=" N   TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.329  1.380 -0.051 1.40e-02 5.10e+03 1.33e+01
  bond model="   0" pdb=" C   ILE A  78 "
       model="   0" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.379 -0.050 1.40e-02 5.10e+03 1.27e+01
  ... (remaining 2235 not shown)

  Histogram of bond angle deviations from ideal:
       83.62 -    95.61: 7
       95.61 -   107.60: 530
      107.60 -   119.59: 2679
      119.59 -   131.58: 848
      131.58 -   143.58: 11
  Bond angle restraints: 4075
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  79 "
        model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  143.58  -21.88 1.80e+00 3.09e-01 1.48e+02
  angle model="   0" pdb=" C   LEU A  93 "
        model="   0" pdb=" CA  LEU A  93 "
        model="   0" pdb=" CB  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.10  132.85  -22.75 1.90e+00 2.77e-01 1.43e+02
  angle model="   0" pdb=" C   THR A  92 "
        model="   0" pdb=" N   LEU A  93 "
        model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     121.70  140.98  -19.28 1.80e+00 3.09e-01 1.15e+02
  angle model="   0" pdb=" C   ILE A  78 "
        model="   0" pdb=" N   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  140.94  -19.24 1.80e+00 3.09e-01 1.14e+02
  angle model="   0" pdb=" CA  THR A  92 "
        model="   0" pdb=" C   THR A  92 "
        model="   0" pdb=" N   LEU A  93 "
      ideal   model   delta    sigma   weight residual
     116.20   95.98   20.22 2.00e+00 2.50e-01 1.02e+02
  ... (remaining 4070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.18: 943
       20.18 -    40.35: 54
       40.35 -    60.53: 21
       60.53 -    80.71: 5
       80.71 -   100.88: 1
  Dihedral angle restraints: 1024
    sinusoidal: 561
      harmonic: 463
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  51 "
           model="   0" pdb=" C   ILE A  51 "
           model="   0" pdb=" N   PRO A  52 "
           model="   0" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   79.12  100.88     0      5.00e+00 4.00e-02 4.07e+02
  dihedral model="   0" pdb=" CA  ILE A  77 "
           model="   0" pdb=" C   ILE A  77 "
           model="   0" pdb=" N   ILE A  78 "
           model="   0" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -104.61  -75.39     0      5.00e+00 4.00e-02 2.27e+02
  dihedral model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" CB  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  154.69  -31.29     0      2.50e+00 1.60e-01 1.57e+02
  ... (remaining 1021 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.139: 169
       1.139 -    2.276: 2
       2.276 -    3.414: 0
       3.414 -    4.552: 2
       4.552 -    5.689: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CB  ILE A  78 "
            model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" CG1 ILE A  78 "
            model="   0" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -3.04    5.69 2.00e-01 2.50e+01 8.09e+02
  chirality model="   0" pdb=" CA  LYS A  79 "
            model="   0" pdb=" N   LYS A  79 "
            model="   0" pdb=" C   LYS A  79 "
            model="   0" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.16    5.67 2.00e-01 2.50e+01 8.03e+02
  chirality model="   0" pdb=" CA  TYR A  89 "
            model="   0" pdb=" N   TYR A  89 "
            model="   0" pdb=" C   TYR A  89 "
            model="   0" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.64    5.15 2.00e-01 2.50e+01 6.62e+02
  ... (remaining 173 not shown)

  Planarity restraints: 325
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.150 2.00e-02 2.50e+03   6.02e-02 1.09e+02
        model="   0" pdb=" CG  TYR A 111 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.104 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.112 2.00e-02 2.50e+03   4.88e-02 7.16e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.095 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.042 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.106 2.00e-02 2.50e+03   4.09e-02 5.02e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 322 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 139
        2.15 -     2.77: 4093
   Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.415, 56.567, 48.844, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
       2.77 -     3.38: 6481
        3.38 -     3.99: 7971
        3.99 -     4.60: 12108
  Nonbonded interactions: 30792
  Sorted by model distance:
  nonbonded model="   0" pdb=" HA  ILE A  77 "
            model="   0" pdb=" H   LYS A  79 "
     model   vdw
     1.543 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.704 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.782 1.850
  nonbonded model="   0" pdb=" HA  LYS A  79 "
            model="   0" pdb="HD13 LEU A  93 "
     model   vdw
     1.786 2.440
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.790 1.850
  ... (remaining 30787 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   8" pdb=" N   MET A   1 "
       model="   8" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.459  0.032 2.10e-02 2.27e+03 2.31e+00
  bond model="   8" pdb=" CZ  ARG A 129 "
       model="   8" pdb=" NH1 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.323  1.327 -0.004 1.40e-02 5.10e+03 6.59e-02
  bond model="   8" pdb=" NE  ARG A 129 "
       model="   8" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 5.64e-02
  bond model="   8" pdb=" CZ  ARG A  58 "
       model="   8" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.62e-02
  bond model="   8" pdb=" NE  ARG A  58 "
       model="   8" pdb=" CZ  ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 5.43e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.89 -   106.88: 63
      106.88 -   112.88: 2722
      112.88 -   118.87: 426
      118.87 -   124.87: 824
      124.87 -   130.86: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   8" pdb=" CB  PRO A 102 "
        model="   8" pdb=" CA  PRO A 102 "
        model="   8" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   8" pdb=" CB  PRO A  22 "
        model="   8" pdb=" CA  PRO A  22 "
        model="   8" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  angle model="   8" pdb=" CB  PRO A 114 "
        model="   8" pdb=" CA  PRO A 114 "
        model="   8" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  angle model="   8" pdb=" CB  PRO A  54 "
        model="   8" pdb=" CA  PRO A  54 "
        model="   8" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  angle model="   8" pdb=" CB  PRO A  52 "
        model="   8" pdb=" CA  PRO A  52 "
        model="   8" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.78   -4.78 3.00e+00 1.11e-01 2.53e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 881
       17.93 -    35.85: 74
       35.85 -    53.78: 52
       53.78 -    71.71: 18
       71.71 -    89.64: 7
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   8" pdb=" CA  ASP A  88 "
           model="   8" pdb=" CB  ASP A  88 "
           model="   8" pdb=" CG  ASP A  88 "
           model="   8" pdb=" OD1 ASP A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.32   58.32     1      2.00e+01 2.50e-03 1.14e+01
  dihedral model="   8" pdb=" CA  ASP A  23 "
           model="   8" pdb=" CB  ASP A  23 "
           model="   8" pdb=" CG  ASP A  23 "
           model="   8" pdb=" OD1 ASP A  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.55   57.55     1      2.00e+01 2.50e-03 1.11e+01
  dihedral model="   8" pdb=" CB  GLU A  49 "
           model="   8" pdb=" CG  GLU A  49 "
           model="   8" pdb=" CD  GLU A  49 "
           model="   8" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.64   89.64     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 99
       0.019 -    0.038: 54
       0.038 -    0.057: 4
       0.057 -    0.076: 0
       0.076 -    0.095: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  ILE A 131 "
            model="   8" pdb=" N   ILE A 131 "
            model="   8" pdb=" C   ILE A 131 "
            model="   8" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.24e-01
  chirality model="   8" pdb=" CA  ILE A  71 "
            model="   8" pdb=" N   ILE A  71 "
            model="   8" pdb=" C   ILE A  71 "
            model="   8" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.20e-01
  chirality model="   8" pdb=" CA  ILE A   4 "
            model="   8" pdb=" N   ILE A   4 "
            model="   8" pdb=" C   ILE A   4 "
            model="   8" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.19e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  81 "    0.000 2.00e-02 2.50e+03   1.11e-03 3.73e-02
        model="   8" pdb=" CG  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  81 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  81 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  81 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  89 "    0.000 2.00e-02 2.50e+03   1.07e-03 3.42e-02
        model="   8" pdb=" CG  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  89 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  91 "   -0.001 2.00e-02 2.50e+03   8.69e-04 2.27e-02
        model="   8" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 83
        2.09 -     2.72: 4045
        2.72 -     3.35: 6166
        3.35 -     3.97: 7447
        3.97 -     4.60: 11351
  Nonbonded interactions: 29092
  Sorted by model distance:
  nonbonded model="   8" pdb="HD13 LEU A   3 "
            model="   8" pdb="HD22 LEU A  53 "
     model   vdw
     1.464 2.440
  nonbonded model="   8" pdb="HD11 LEU A  93 "
            model="   8" pdb="HD13 LEU A  99 "
     model   vdw
     1.595 2.440
  nonbonded model="   8" pdb="HD23 LEU A   9 "
            model="   8" pdb="HD22 LEU A  26 "
     model   vdw
     1.612 2.440
  nonbonded model="   8" pdb="HG13 VAL A  41 "
            model="   8" pdb="HD12 ILE A 108 "
     model   vdw
     1.755 2.440
  nonbonded model="   8" pdb="HG12 VAL A  41 "
            model="   8" pdb="HG22 VAL A 112 "
     model   vdw
     1.808 2.440
  ... (remaining 29087 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 73
        1.23 -     1.42: 399
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" CD2 HIS A 134 "
       model="  11" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.92e+00
  bond model="  11" pdb=" CD2 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.62e+00
  bond model="  11" pdb=" CZ  ARG A  58 "
       model="  11" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.39e+00
  bond model="  11" pdb=" CD2 HIS A 136 "
       model="  11" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.37e+00
  bond model="  11" pdb=" CE1 HIS A 135 "
       model="  11" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.31e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.80 -   106.34: 145
      106.34 -   112.88: 2570
      112.88 -   119.41: 544
      119.41 -   125.95: 782
      125.95 -   132.49: 38
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" OE1 GLN A  66 "
        model="  11" pdb=" CD  GLN A  66 "
        model="  11" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  115.05    7.55 1.00e+00 1.00e+00 5.71e+01
  angle model="  11" pdb=" CA  ASP A  47 "
        model="  11" pdb=" CB  ASP A  47 "
        model="  11" pdb=" CG  ASP A  47 "
      ideal   model   delta    sigma   weight residual
     112.60  106.46    6.14 1.00e+00 1.00e+00 3.77e+01
  angle model="  11" pdb=" CA  ASP A 116 "
        model="  11" pdb=" CB  ASP A 116 "
        model="  11" pdb=" CG  ASP A 116 "
      ideal   model   delta    sigma   weight residual
     112.60  107.13    5.47 1.00e+00 1.00e+00 2.99e+01
  angle model="  11" pdb=" OE1 GLN A 100 "
        model="  11" pdb=" CD  GLN A 100 "
        model="  11" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.18    4.42 1.00e+00 1.00e+00 1.96e+01
  angle model="  11" pdb=" CA  LYS A 101 "
        model="  11" pdb=" C   LYS A 101 "
        model="  11" pdb=" N   PRO A 102 "
      ideal   model   delta    sigma   weight residual
     116.90  122.99   -6.09 1.50e+00 4.44e-01 1.65e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 914
       17.49 -    34.99: 78
       34.99 -    52.48: 32
       52.48 -    69.98: 8
       69.98 -    87.47: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  11" pdb=" C   ARG A 129 "
           model="  11" pdb=" N   ARG A 129 "
           model="  11" pdb=" CA  ARG A 129 "
           model="  11" pdb=" CB  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.27   16.67     0      2.50e+00 1.60e-01 4.44e+01
  dihedral model="  11" pdb=" N   ARG A 129 "
           model="  11" pdb=" C   ARG A 129 "
           model="  11" pdb=" CA  ARG A 129 "
           model="  11" pdb=" CB  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.95  -16.15     0      2.50e+00 1.60e-01 4.17e+01
  dihedral model="  11" pdb=" CA  VAL A 112 "
           model="  11" pdb=" C   VAL A 112 "
           model="  11" pdb=" N   LYS A 113 "
           model="  11" pdb=" CA  LYS A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.84   31.16     0      5.00e+00 4.00e-02 3.88e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.134: 147
       0.134 -    0.267: 26
       0.267 -    0.401: 2
       0.401 -    0.535: 0
       0.535 -    0.668: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  ARG A 129 "
            model="  11" pdb=" N   ARG A 129 "
            model="  11" pdb=" C   ARG A 129 "
            model="  11" pdb=" CB  ARG A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.84    0.67 2.00e-01 2.50e+01 1.12e+01
  chirality model="  11" pdb=" CA  HIS A 134 "
            model="  11" pdb=" N   HIS A 134 "
            model="  11" pdb=" C   HIS A 134 "
            model="  11" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.35e+00
  chirality model="  11" pdb=" CA  TYR A 111 "
            model="  11" pdb=" N   TYR A 111 "
            model="  11" pdb=" C   TYR A 111 "
            model="  11" pdb=" CB  TYR A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.16e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  91 "    0.376 2.00e-02 2.50e+03   1.58e-01 7.45e+02
        model="  11" pdb=" CG  TYR A  91 "   -0.055 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  91 "   -0.088 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  91 "   -0.072 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  91 "   -0.040 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  91 "   -0.062 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  91 "    0.307 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  91 "   -0.142 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  91 "   -0.091 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  91 "   -0.043 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  91 "   -0.103 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  89 "    0.370 2.00e-02 2.50e+03   1.48e-01 6.56e+02
        model="  11" pdb=" CG  TYR A  89 "   -0.057 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  89 "   -0.082 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  89 "   -0.081 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  89 "   -0.042 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  89 "   -0.036 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  89 "    0.030 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  89 "    0.260 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  89 "   -0.124 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  89 "   -0.127 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  89 "   -0.062 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  89 "   -0.049 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A 111 "    0.193 2.00e-02 2.50e+03   9.79e-02 2.88e+02
        model="  11" pdb=" CG  TYR A 111 "   -0.053 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A 111 "   -0.087 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A 111 "    0.039 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A 111 "   -0.032 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A 111 "    0.025 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A 111 "    0.044 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A 111 "   -0.193 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A 111 "    0.024 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A 111 "    0.133 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A 111 "   -0.080 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 162
        2.19 -     2.79: 4248
        2.79 -     3.40: 6010
        3.40 -     4.00: 7014
        4.00 -     4.60: 10687
  Nonbonded interactions: 28121
  Sorted by model distance:
  nonbonded model="  11" pdb=" HD2 PHE A  15 "
            model="  11" pdb="HE21 GLN A  66 "
     model   vdw
     1.591 2.100
  nonbonded model="  11" pdb="HG21 THR A  83 "
            model="  11" pdb=" HD2 TYR A  91 "
     model   vdw
     1.610 2.270
  nonbonded model="  11" pdb=" HZ  PHE A  15 "
            model="  11" pdb="HG23 THR A  83 "
     model   vdw
     1.695 2.270
  nonbonded model="  11" pdb=" HZ2 LYS A  63 "
            model="  11" pdb=" OD2 ASP A 110 "
     model   vdw
     1.754 1.850
  nonbonded model="  11" pdb=" OE2 GLU A  16 "
            model="  11" pdb=" HZ2 LYS A  19 "
     model   vdw
     1.812 1.850
  ... (remaining 28116 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  14" pdb=" CB  SER A  76 "
        model="  14" pdb=" CB  TYR A  91 "
        model="  14" pdb=" CB  ASP A 103 "
  Number of C-beta restraints generated:  258

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.154, 44.151, 63.417, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   8" pdb=" N   MET A   1 "
       model="   8" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.42e+00
  bond model="   8" pdb=" CZ  ARG A 127 "
       model="   8" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.326  0.004 1.30e-02 5.92e+03 7.39e-02
  bond model="   8" pdb=" NE  ARG A  58 "
       model="   8" pdb=" CZ  ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 6.92e-02
  bond model="   8" pdb=" CZ  ARG A 129 "
       model="   8" pdb=" NH1 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.323  1.327 -0.004 1.40e-02 5.10e+03 6.57e-02
  bond model="   8" pdb=" CZ  ARG A  58 "
       model="   8" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.41e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.90 -   106.90: 68
      106.90 -   112.90: 2717
      112.90 -   118.90: 426
      118.90 -   124.90: 824
      124.90 -   130.90: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   8" pdb=" CB  PRO A 117 "
        model="   8" pdb=" CA  PRO A 117 "
        model="   8" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.86   -4.86 3.00e+00 1.11e-01 2.62e+00
  angle model="   8" pdb=" CB  PRO A  22 "
        model="   8" pdb=" CA  PRO A  22 "
        model="   8" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   8" pdb=" CB  PRO A 114 "
        model="   8" pdb=" CA  PRO A 114 "
        model="   8" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   8" pdb=" CB  PRO A 102 "
        model="   8" pdb=" CA  PRO A 102 "
        model="   8" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   8" pdb=" CB  PRO A  54 "
        model="   8" pdb=" CA  PRO A  54 "
        model="   8" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.78   -4.78 3.00e+00 1.11e-01 2.54e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 884
       17.73 -    35.46: 87
       35.46 -    53.19: 40
       53.19 -    70.92: 16
       70.92 -    88.65: 5
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   8" pdb=" CB  GLU A  24 "
           model="   8" pdb=" CG  GLU A  24 "
           model="   8" pdb=" CD  GLU A  24 "
           model="   8" pdb=" OE1 GLU A  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.10  -85.10     1      3.00e+01 1.11e-03 9.75e+00
  dihedral model="   8" pdb=" N   ASP A 116 "
           model="   8" pdb=" CA  ASP A 116 "
           model="   8" pdb=" CB  ASP A 116 "
           model="   8" pdb=" CG  ASP A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.02  -59.98     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   8" pdb=" CA  GLU A 123 "
           model="   8" pdb=" CB  GLU A 123 "
           model="   8" pdb=" CG  GLU A 123 "
           model="   8" pdb=" CD  GLU A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.59  -59.41     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 107
       0.019 -    0.039: 47
       0.039 -    0.058: 3
       0.058 -    0.077: 0
       0.077 -    0.097: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  ILE A  51 "
            model="   8" pdb=" N   ILE A  51 "
            model="   8" pdb=" C   ILE A  51 "
            model="   8" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.34e-01
  chirality model="   8" pdb=" CA  ILE A  77 "
            model="   8" pdb=" N   ILE A  77 "
            model="   8" pdb=" C   ILE A  77 "
            model="   8" pdb=" CB  ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.25e-01
  chirality model="   8" pdb=" CA  ILE A  38 "
            model="   8" pdb=" N   ILE A  38 "
            model="   8" pdb=" C   ILE A  38 "
            model="   8" pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.24e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A 105 "   -0.000 2.00e-02 2.50e+03   1.40e-03 5.85e-02
        model="   8" pdb=" CG  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A 105 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A 105 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A 105 "    0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A 105 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  PHE A  45 "    0.001 2.00e-02 2.50e+03   1.18e-03 4.20e-02
        model="   8" pdb=" CG  PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 PHE A  45 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 PHE A  45 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HZ  PHE A  45 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  81 "   -0.000 2.00e-02 2.50e+03   1.11e-03 3.72e-02
        model="   8" pdb=" CG  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  81 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  81 "    0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 271
        2.23 -     2.82: 4901
        2.82 -     3.42: 5699
        3.42 -     4.01: 7144
        4.01 -     4.60: 10691
  Nonbonded interactions: 28706
  Sorted by model distance:
  nonbonded model="   8" pdb="HG23 ILE A  37 "
            model="   8" pdb="HD13 ILE A 108 "
     model   vdw
     1.638 2.440
  nonbonded model="   8" pdb="HG13 VAL A  41 "
            model="   8" pdb="HD12 ILE A 108 "
     model   vdw
     1.695 2.440
  nonbonded model="   8" pdb="HD23 LEU A   9 "
            model="   8" pdb="HD22 LEU A  26 "
     model   vdw
     1.741 2.440
  nonbonded model="   8" pdb=" HA  LYS A  27 "
            model="   8" pdb="HD12 ILE A  30 "
     model   vdw
     1.753 2.440
  nonbonded model="   8" pdb="HG22 ILE A  78 "
            model="   8" pdb=" H   GLY A  80 "
     model   vdw
     1.754 2.270
  ... (remaining 28701 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 89
        1.23 -     1.42: 383
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" CZ  ARG A 127 "
       model="  14" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.00e+00
  bond model="  14" pdb=" CD2 HIS A 134 "
       model="  14" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.50e+00
  bond model="  14" pdb=" CB  THR A  56 "
       model="  14" pdb=" OG1 THR A  56 "
    ideal  model  delta    sigma   weight residual
    1.433  1.392  0.041 1.60e-02 3.91e+03 6.46e+00
  bond model="  14" pdb=" CD2 HIS A 135 "
       model="  14" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.41e+00
  bond model="  14" pdb=" CZ  ARG A  58 "
       model="  14" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.35e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       93.33 -   101.30: 8
      101.30 -   109.27: 1133
      109.27 -   117.24: 1898
      117.24 -   125.21: 984
      125.21 -   133.18: 56
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" CA  ASP A  44 "
        model="  14" pdb=" CB  ASP A  44 "
        model="  14" pdb=" CG  ASP A  44 "
      ideal   model   delta    sigma   weight residual
     112.60  120.67   -8.07 1.00e+00 1.00e+00 6.51e+01
  angle model="  14" pdb=" CA  ASP A 103 "
        model="  14" pdb=" CB  ASP A 103 "
        model="  14" pdb=" CG  ASP A 103 "
      ideal   model   delta    sigma   weight residual
     112.60  119.07   -6.47 1.00e+00 1.00e+00 4.18e+01
  angle model="  14" pdb=" C   PRO A 102 "
        model="  14" pdb=" N   ASP A 103 "
        model="  14" pdb=" CA  ASP A 103 "
      ideal   model   delta    sigma   weight residual
     121.70  133.18  -11.48 1.80e+00 3.09e-01 4.07e+01
  angle model="  14" pdb=" C   ASP A 103 "
        model="  14" pdb=" CA  ASP A 103 "
        model="  14" pdb=" HA  ASP A 103 "
      ideal   model   delta    sigma   weight residual
     109.00   93.33   15.67 3.00e+00 1.11e-01 2.73e+01
  angle model="  14" pdb=" C   TYR A  91 "
        model="  14" pdb=" CA  TYR A  91 "
        model="  14" pdb=" HA  TYR A  91 "
      ideal   model   delta    sigma   weight residual
     109.00   94.06   14.94 3.00e+00 1.11e-01 2.48e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 923
       17.06 -    34.11: 62
       34.11 -    51.17: 26
       51.17 -    68.23: 8
       68.23 -    85.28: 8
  Dihedral angle restraints: 1027
    sinusoidal: 562
      harmonic: 465
  Sorted by residual:
  dihedral model="  14" pdb=" CA  SER A  90 "
           model="  14" pdb=" C   SER A  90 "
           model="  14" pdb=" N   TYR A  91 "
           model="  14" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  122.89   57.11     0      5.00e+00 4.00e-02 1.30e+02
  dihedral model="  14" pdb=" CA  GLU A  75 "
           model="  14" pdb=" C   GLU A  75 "
           model="  14" pdb=" N   SER A  76 "
           model="  14" pdb=" CA  SER A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.05   24.95     0      5.00e+00 4.00e-02 2.49e+01
  dihedral model="  14" pdb=" N   PRO A 102 "
           model="  14" pdb=" C   PRO A 102 "
           model="  14" pdb=" CA  PRO A 102 "
           model="  14" pdb=" CB  PRO A 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  127.32  -12.22     0      2.50e+00 1.60e-01 2.39e+01
  ... (remaining 1024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.851: 173
       0.851 -    1.700: 0
       1.700 -    2.549: 0
       2.549 -    3.399: 0
       3.399 -    4.248: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CA  TYR A  91 "
            model="  14" pdb=" N   TYR A  91 "
            model="  14" pdb=" C   TYR A  91 "
            model="  14" pdb=" CB  TYR A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.74    4.25 2.00e-01 2.50e+01 4.51e+02
  chirality model="  14" pdb=" CA  SER A  76 "
            model="  14" pdb=" N   SER A  76 "
            model="  14" pdb=" C   SER A  76 "
            model="  14" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.63    4.14 2.00e-01 2.50e+01 4.29e+02
  chirality model="  14" pdb=" CA  ASP A 103 "
            model="  14" pdb=" N   ASP A 103 "
            model="  14" pdb=" C   ASP A 103 "
            model="  14" pdb=" CB  ASP A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.51    4.02 2.00e-01 2.50e+01 4.05e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  50 "    0.114 2.00e-02 2.50e+03   5.43e-02 8.85e+01
        model="  14" pdb=" CG  TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  50 "    0.109 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  50 "   -0.037 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  50 "   -0.069 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  50 "   -0.045 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  89 "   -0.097 2.00e-02 2.50e+03   4.55e-02 6.20e+01
        model="  14" pdb=" CG  TYR A  89 "   -0.021 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  89 "    0.029 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  89 "    0.014 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  89 "   -0.025 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  89 "   -0.060 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  89 "    0.083 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  89 "    0.033 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  89 "    0.041 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  TYR A  12 "   -0.108 2.00e-02 2.50e+03   4.45e-02 5.94e+01
        model="  14" pdb=" CG  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 TYR A  12 "    0.025 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 TYR A  12 "    0.022 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="  14" pdb=" OH  TYR A  12 "   -0.074 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 TYR A  12 "    0.050 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 TYR A  12 "    0.040 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 TYR A  12 "    0.024 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 120
        2.14 -     2.76: 3889
        2.76 -     3.37: 6112
        3.37 -     3.99: 7292
        3.99 -     4.60: 10876
  Nonbonded interactions: 28289
  Sorted by model distance:
  nonbonded model="  14" pdb=" H   GLY A 121 "
            model="  14" pdb="HD22 LEU A 132 "
     model   vdw
     1.527 2.270
  nonbonded model="  14" pdb=" HA  PRO A 102 "
            model="  14" pdb=" H   ASP A 103 "
     model   vdw
     1.772 2.270
  nonbonded model="  14" pdb=" OD2 ASP A  36 "
            model="  14" pdb=" HZ1 LYS A  40 "
     model   vdw
     1.796 1.850
  nonbonded model="  14" pdb=" HD2 TYR A 105 "
            model="  14" pdb="HG23 ILE A 122 "
     model   vdw
     1.811 2.270
  nonbonded model="  14" pdb=" OD1 ASP A  44 "
            model="  14" pdb=" HG  SER A  46 "
     model   vdw
     1.831 1.850
  ... (remaining 28284 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  THR A  92 "
        model="   5" pdb=" CB  SER A  98 "
  Number of C-beta restraints generated:  258

  Time building geometry restraints manager: 0.73 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   61": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.404, 39.317, 51.827, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  MET A   1 "
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  LYS A  79 "
        model="   7" pdb=" CB  GLU A 120 "
        model="   7" pdb=" CB  GLU A 123 "
        model="   7" pdb=" CB  VAL A 126 "
        model="   7" pdb=" CB  ARG A 127 "
        model="   7" pdb=" CB  MET A 128 "
        model="   7" pdb=" CB  LEU A 132 "
        model="   7" pdb=" CB  GLU A 133 "
        model="   7" pdb=" CB  HIS A 135 "
        model="   7" pdb=" CB  HIS A 138 "
  Number of C-beta restraints generated:  240

  Time building geometry restraints manager: 0.98 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 47
        1.23 -     1.43: 425
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" N   LEU A  99 "
       model="   5" pdb=" CA  LEU A  99 "
    ideal  model  delta    sigma   weight residual
    1.458  1.516 -0.058 1.90e-02 2.77e+03 9.41e+00
  bond model="   5" pdb=" N   ILE A  77 "
       model="   5" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.514 -0.056 1.90e-02 2.77e+03 8.73e+00
  bond model="   5" pdb=" CA  SER A  98 "
       model="   5" pdb=" C   SER A  98 "
    ideal  model  delta    sigma   weight residual
    1.525  1.584 -0.059 2.10e-02 2.27e+03 7.86e+00
  bond model="   5" pdb=" CZ  ARG A  21 "
       model="   5" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.78e+00
  bond model="   5" pdb=" CD2 HIS A 137 "
       model="   5" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.52e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       88.65 -    98.33: 6
       98.33 -   108.01: 566
      108.01 -   117.69: 2513
      117.69 -   127.38: 970
      127.38 -   137.06: 24
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" C   SER A  98 "
        model="   5" pdb=" CA  SER A  98 "
        model="   5" pdb=" CB  SER A  98 "
      ideal   model   delta    sigma   weight residual
     110.10  132.94  -22.84 1.90e+00 2.77e-01 1.44e+02
  angle model="   5" pdb=" C   HIS A 138 "
        model="   5" pdb=" N   HIS A 139 "
        model="   5" pdb=" CA  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     121.70  137.06  -15.36 1.80e+00 3.09e-01 7.28e+01
  angle model="   5" pdb=" CA  ILE A  51 "
        model="   5" pdb=" C   ILE A  51 "
        model="   5" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  127.89  -10.99 1.50e+00 4.44e-01 5.37e+01
  angle model="   5" pdb=" C   SER A  98 "
        model="   5" pdb=" CA  SER A  98 "
        model="   5" pdb=" HA  SER A  98 "
      ideal   model   delta    sigma   weight residual
     109.00   88.65   20.35 3.00e+00 1.11e-01 4.60e+01
  angle model="   5" pdb=" N   LEU A  93 "
        model="   5" pdb=" CA  LEU A  93 "
        model="   5" pdb=" CB  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.50  121.56  -11.06 1.70e+00 3.46e-01 4.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 939
       17.47 -    34.93: 59
       34.93 -    52.40: 20
       52.40 -    69.86: 7
       69.86 -    87.33: 2
  Dihedral angle restraints: 1027
    sinusoidal: 562
      harmonic: 465
  Sorted by residual:
  dihedral model="   5" pdb=" CA  THR A  92 "
           model="   5" pdb=" C   THR A  92 "
           model="   5" pdb=" N   LEU A  93 "
           model="   5" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -98.65  -81.35     0      5.00e+00 4.00e-02 2.65e+02
  dihedral model="   5" pdb=" CA  SER A  76 "
           model="   5" pdb=" C   SER A  76 "
           model="   5" pdb=" N   ILE A  77 "
           model="   5" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  115.48   64.52     0      5.00e+00 4.00e-02 1.67e+02
  dihedral model="   5" pdb=" CA  SER A  98 "
           model="   5" pdb=" C   SER A  98 "
           model="   5" pdb=" N   LEU A  99 "
           model="   5" pdb=" CA  LEU A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  128.72   51.28     0      5.00e+00 4.00e-02 1.05e+02
  ... (remaining 1024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.048: 173
       1.048 -    2.096: 0
       2.096 -    3.143: 0
       3.143 -    4.191: 2
       4.191 -    5.239: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CA  THR A  92 "
            model="   5" pdb=" N   THR A  92 "
            model="   5" pdb=" C   THR A  92 "
            model="   5" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.71    5.24 2.00e-01 2.50e+01 6.86e+02
  chirality model="   5" pdb=" CA  SER A  98 "
            model="   5" pdb=" N   SER A  98 "
            model="   5" pdb=" C   SER A  98 "
            model="   5" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.48    3.99 2.00e-01 2.50e+01 3.99e+02
  chirality model="   5" pdb=" CA  ILE A  51 "
            model="   5" pdb=" N   ILE A  51 "
            model="   5" pdb=" C   ILE A  51 "
            model="   5" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -1.10    3.53 2.00e-01 2.50e+01 3.11e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A 111 "   -0.124 2.00e-02 2.50e+03   4.97e-02 7.40e+01
        model="   5" pdb=" CG  TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A 111 "    0.030 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A 111 "    0.026 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A 111 "   -0.086 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A 111 "    0.047 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A 111 "    0.036 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A 111 "    0.024 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  PHE A  67 "   -0.124 2.00e-02 2.50e+03   4.72e-02 6.70e+01
        model="   5" pdb=" CG  PHE A  67 "    0.031 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 PHE A  67 "    0.030 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 PHE A  67 "    0.033 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 PHE A  67 "    0.004 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  PHE A  67 "   -0.021 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 PHE A  67 "    0.046 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 PHE A  67 "    0.056 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 PHE A  67 "    0.003 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 PHE A  67 "   -0.006 2.00e-02 2.50e+03
        model="   5" pdb=" HZ  PHE A  67 "   -0.052 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  12 "   -0.097 2.00e-02 2.50e+03   4.38e-02 5.76e+01
        model="   5" pdb=" CG  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  12 "   -0.090 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  12 "    0.044 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  12 "    0.039 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.20: 177
        2.20 -     2.80: 4410
   Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 90
        1.23 -     1.43: 382
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" CD2 HIS A 139 "
       model="  12" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.98e+00
  bond model="  12" pdb=" CD2 HIS A 136 "
       model="  12" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.83e+00
  bond model="  12" pdb=" CZ  ARG A  21 "
       model="  12" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.46e+00
  bond model="  12" pdb=" CE1 HIS A 138 "
       model="  12" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.97e+00
  bond model="  12" pdb=" CD2 HIS A 138 "
       model="  12" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.77e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.94 -   105.06: 59
      105.06 -   111.17: 2362
      111.17 -   117.29: 632
      117.29 -   123.40: 858
      123.40 -   129.52: 168
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" CA  ASP A 103 "
        model="  12" pdb=" CB  ASP A 103 "
        model="  12" pdb=" CG  ASP A 103 "
      ideal   model   delta    sigma   weight residual
     112.60  119.32   -6.72 1.00e+00 1.00e+00 4.51e+01
  angle model="  12" pdb=" NE  ARG A 127 "
        model="  12" pdb=" CZ  ARG A 127 "
        model="  12" pdb=" NH2 ARG A 127 "
      ideal   model   delta    sigma   weight residual
     119.20  124.29   -5.09 9.00e-01 1.23e+00 3.20e+01
  angle model="  12" pdb=" CA  LYS A 101 "
        model="  12" pdb=" C   LYS A 101 "
        model="  12" pdb=" N   PRO A 102 "
      ideal   model   delta    sigma   weight residual
     116.90  123.91   -7.01 1.50e+00 4.44e-01 2.19e+01
  angle model="  12" pdb=" OE1 GLN A 100 "
        model="  12" pdb=" CD  GLN A 100 "
        model="  12" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.19    4.41 1.00e+00 1.00e+00 1.95e+01
  angle model="  12" pdb=" NH1 ARG A 127 "
        model="  12" pdb=" CZ  ARG A 127 "
        model="  12" pdb=" NH2 ARG A 127 "
      ideal   model   delta    sigma   weight residual
     119.30  113.67    5.63 1.30e+00 5.92e-01 1.88e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.18: 893
       14.18 -    28.37: 94
       28.37 -    42.55: 29
       42.55 -    56.73: 10
       56.73 -    70.91: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  12" pdb=" CA  LYS A 101 "
           model="  12" pdb=" C   LYS A 101 "
           model="  12" pdb=" N   PRO A 102 "
           model="  12" pdb=" CA  PRO A 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.81  -29.19     0      5.00e+00 4.00e-02 3.41e+01
  dihedral model="  12" pdb=" CA  GLY A  94 "
           model="  12" pdb=" C   GLY A  94 "
           model="  12" pdb=" N   ASP A  95 "
           model="  12" pdb=" CA  ASP A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.65  -25.35     0      5.00e+00 4.00e-02 2.57e+01
  dihedral model="  12" pdb=" CA  MET A   1 "
           model="  12" pdb=" C   MET A   1 "
           model="  12" pdb=" N   LEU A   2 "
           model="  12" pdb=" CA  LEU A   2 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.14  -20.86     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 98
       0.082 -    0.163: 67
       0.163 -    0.244: 9
       0.244 -    0.326: 1
             2.80 -     3.40: 6237
        3.40 -     4.00: 7582
        4.00 -     4.60: 11353
  Nonbonded interactions: 29759
  Sorted by model distance:
  nonbonded model="   5" pdb="HG23 ILE A  77 "
            model="   5" pdb=" H   LEU A  99 "
     model   vdw
     1.606 2.270
  nonbonded model="   5" pdb=" H   LEU A  93 "
            model="   5" pdb=" HA  LEU A  99 "
     model   vdw
     1.637 2.270
  nonbonded model="   5" pdb="HG22 ILE A  77 "
            model="   5" pdb="HG23 ILE A  78 "
     model   vdw
     1.658 2.440
  nonbonded model="   5" pdb=" H   SER A  97 "
            model="   5" pdb=" H   SER A  98 "
     model   vdw
     1.660 2.100
  nonbonded model="   5" pdb="HG22 ILE A  71 "
            model="   5" pdb="HG21 ILE A  77 "
     model   vdw
     1.741 2.440
  ... (remaining 29754 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
 0.326 -    0.407: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  PRO A 102 "
            model="  12" pdb=" N   PRO A 102 "
            model="  12" pdb=" C   PRO A 102 "
            model="  12" pdb=" CB  PRO A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.31    0.41 2.00e-01 2.50e+01 4.14e+00
  chirality model="  12" pdb=" CA  ASP A  95 "
            model="  12" pdb=" N   ASP A  95 "
            model="  12" pdb=" C   ASP A  95 "
            model="  12" pdb=" CB  ASP A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality model="  12" pdb=" CA  THR A  83 "
            model="  12" pdb=" N   THR A  83 "
            model="  12" pdb=" C   THR A  83 "
            model="  12" pdb=" CB  THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.30    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  81 "   -0.223 2.00e-02 2.50e+03   1.20e-01 4.35e+02
        model="  12" pdb=" CG  TYR A  81 "   -0.029 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  81 "    0.038 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  81 "    0.040 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  81 "    0.057 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  81 "    0.052 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  81 "   -0.004 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  81 "   -0.286 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  81 "    0.071 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  81 "    0.077 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  81 "    0.110 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  81 "    0.097 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  PHE A  67 "   -0.317 2.00e-02 2.50e+03   1.20e-01 4.34e+02
        model="  12" pdb=" CG  PHE A  67 "    0.070 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 PHE A  67 "    0.077 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 PHE A  67 "    0.083 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 PHE A  67 "    0.007 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  PHE A  67 "   -0.050 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 PHE A  67 "    0.129 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 PHE A  67 "    0.144 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 PHE A  67 "   -0.002 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 PHE A  67 "   -0.018 2.00e-02 2.50e+03
        model="  12" pdb=" HZ  PHE A  67 "   -0.123 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  91 "    0.037 2.00e-02 2.50e+03   4.61e-02 6.39e+01
        model="  12" pdb=" CG  TYR A  91 "   -0.020 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  91 "   -0.034 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  91 "    0.035 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  91 "   -0.005 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  91 "   -0.047 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  91 "   -0.089 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  91 "    0.031 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  91 "    0.098 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  91 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 379
        2.30 -     2.87: 5118
        2.87 -     3.45: 5561
        3.45 -     4.02: 7004
        4.02 -     4.60: 10373
  Nonbonded interactions: 28435
  Sorted by model distance:
  nonbonded model="  12" pdb=" OD2 ASP A  36 "
            model="  12" pdb=" HH  TYR A  68 "
     model   vdw
     1.722 1.850
  nonbonded model="  12" pdb=" HA  LEU A   3 "
            model="  12" pdb="HD22 LEU A  53 "
     model   vdw
     1.761 2.440
  nonbonded model="  12" pdb=" OE2 GLU A  16 "
            model="  12" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.806 1.850
  nonbonded model="  12" pdb="HD23 LEU A   2 "
            model="  12" pdb=" H   LEU A   3 "
     model   vdw
     1.831 2.270
  nonbonded model="  12" pdb=" O   GLU A  16 "
            model="  12" pdb=" HG1 THR A  20 "
     model   vdw
     1.838 1.850
  ... (remaining 28430 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 39
        1.23 -     1.42: 442
        1.42 -     1.62: 650
        1.62 -     1.81: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" CA  MET A 128 "
       model="   7" pdb=" CB  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.530  1.661 -0.131 2.00e-02 2.50e+03 4.29e+01
  bond model="   7" pdb=" CA  MET A 128 "
       model="   7" pdb=" C   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.525  1.407  0.118 2.10e-02 2.27e+03 3.14e+01
  bond model="   7" pdb=" N   ARG A 127 "
       model="   7" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.374  0.084 1.90e-02 2.77e+03 1.97e+01
  bond model="   7" pdb=" N   GLY A  80 "
       model="   7" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.518 -0.067 1.60e-02 3.91e+03 1.76e+01
  bond model="   7" pdb=" N   GLU A 123 "
       model="   7" pdb=" CA  GLU A 123 "
    ideal  model  delta    sigma   weight residual
    1.458  1.380  0.078 1.90e-02 2.77e+03 1.67e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       65.16 -    87.01: 2
       87.01 -   108.87: 983
      108.87 -   130.73: 3079
      130.73 -   152.58: 14
      152.58 -   174.44: 1
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" CA  ILE A  51 "
        model="   7" pdb=" C   ILE A  51 "
        model="   7" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  174.44  -57.54 1.50e+00 4.44e-01 1.47e+03
  angle model="   7" pdb=" O   ILE A  51 "
        model="   7" pdb=" C   ILE A  51 "
        model="   7" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     123.00   87.20   35.80 1.60e+00 3.91e-01 5.01e+02
  angle model="   7" pdb=" CA  ILE A  51 "
        model="   7" pdb=" C   ILE A  51 "
        model="   7" pdb=" O   ILE A  51 "
      ideal   model   delta    sigma   weight residual
     120.80   87.30   33.50 1.70e+00 3.46e-01 3.88e+02
  angle model="   7" pdb=" C   ILE A  78 "
        model="   7" pdb=" CA  ILE A  78 "
        model="   7" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   65.16   43.84 3.00e+00 1.11e-01 2.14e+02
  angle model="   7" pdb=" CA  ILE A 122 "
        model="   7" pdb=" CB  ILE A 122 "
        model="   7" pdb=" CG1 ILE A 122 "
      ideal   model   delta    sigma   weight residual
     110.40  134.14  -23.74 1.70e+00 3.46e-01 1.95e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.14: 937
       26.14 -    52.28: 51
       52.28 -    78.41: 14
       78.41 -   104.55: 4
      104.55 -   130.69: 3
  Dihedral angle restraints: 1009
    sinusoidal: 562
      harmonic: 447
  Sorted by residual:
  dihedral model="   7" pdb=" CA  ARG A 127 "
           model="   7" pdb=" C   ARG A 127 "
           model="   7" pdb=" N   MET A 128 "
           model="   7" pdb=" CA  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -49.31 -130.69     0      5.00e+00 4.00e-02 6.83e+02
  dihedral model="   7" pdb=" CA  LYS A  79 "
           model="   7" pdb=" C   LYS A  79 "
           model="   7" pdb=" N   GLY A  80 "
           model="   7" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   56.58  123.42     0      5.00e+00 4.00e-02 6.09e+02
  dihedral model="   7" pdb=" CA  ILE A 122 "
           model="   7" pdb=" C   ILE A 122 "
           model="   7" pdb=" N   GLU A 123 "
           model="   7" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -68.18 -111.82     0      5.00e+00 4.00e-02 5.00e+02
  ... (remaining 1006 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.077: 162
       1.077 -    2.154: 1
       2.154 -    3.231: 0
       3.231 -    4.307: 1
       4.307 -    5.384: 12
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CA  LYS A  79 "
            model="   7" pdb=" N   LYS A  79 "
            model="   7" pdb=" C   LYS A  79 "
            model="   7" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.87    5.38 2.00e-01 2.50e+01 7.25e+02
  chirality model="   7" pdb=" CA  GLU A 123 "
            model="   7" pdb=" N   GLU A 123 "
            model="   7" pdb=" C   GLU A 123 "
            model="   7" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.62    5.13 2.00e-01 2.50e+01 6.57e+02
  chirality model="   7" pdb=" CA  MET A   1 "
            model="   7" pdb=" N   MET A   1 "
            model="   7" pdb=" C   MET A   1 "
            model="   7" pdb=" CB  MET A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57   -2.41    4.97 2.00e-01 2.50e+01 6.19e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  50 "    0.292 2.00e-02 2.50e+03   1.24e-01 4.63e+02
        model="   7" pdb=" CG  TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  50 "   -0.054 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  50 "   -0.068 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  50 "   -0.046 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  50 "   -0.034 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  50 "    0.244 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  50 "   -0.081 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  50 "   -0.121 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  50 "   -0.078 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  50 "   -0.042 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  81 "    0.085 2.00e-02 2.50e+03   3.98e-02 4.76e+01
        model="   7" pdb=" CG  TYR A  81 "   -0.064 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  81 "   -0.035 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  81 "   -0.002 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  81 "    0.030 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  81 "   -0.044 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  81 "    0.024 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  81 "    0.045 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  81 "   -0.023 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  12 "   -0.086 2.00e-02 2.50e+03   3.97e-02 4.73e+01
        model="   7" pdb=" CG  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  12 "    0.018 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  12 "   -0.084 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  12 "    0.039 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  12 "    0.037 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 139
        2.14 -     2.76: 4063
        2.76 -     3.37: 6488
        3.37 -     3.99: 7925
        3.99 -     4.60: 11865
  Nonbonded interactions: 30480
  Sorted by model distance:
  nonbonded model="   7" pdb=" HA  ILE A  78 "
            model="   7" pdb=" HB2 LYS A  79 "
     model   vdw
     1.528 2.440
  nonbonded model="   7" pdb=" H   ILE A 122 "
            model="   7" pdb=" HA  GLU A 123 "
     model   vdw
     1.609 2.270
  nonbonded model="   7" pdb=" HB3 ALA A  48 "
            model="   7" pdb="HG21 ILE A 122 "
     model   vdw
     1.657 2.440
  nonbonded model="   7" pdb=" H   ILE A 122 "
            model="   7" pdb=" H   VAL A 126 "
     model   vdw
     1.679 2.100
  nonbonded model="   7" pdb=" HA  LYS A  79 "
            model="   7" pdb=" H   TYR A  81 "
     model   vdw
     1.698 2.270
  ... (remaining 30475 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   0" pdb=" CB  ILE A  51 "
        model="   0" pdb=" CB  ASP A  74 "
        model="   0" pdb=" CB  SER A  90 "
        model="   0" pdb=" CB  THR A  92 "
        model="   0" pdb=" CB  LEU A  93 "
        model="   0" pdb=" CB  ALA A 124 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.59, 63.226, 55.711, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 73
        1.23 -     1.42: 399
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  14" pdb=" CZ  ARG A  21 "
       model="  14" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.63e+00
  bond model="  14" pdb=" CB  THR A  92 "
       model="  14" pdb=" OG1 THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.433  1.389  0.044 1.60e-02 3.91e+03 7.59e+00
  bond model="  14" pdb=" CD2 HIS A 139 "
       model="  14" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.54e+00
  bond model="  14" pdb=" CE1 HIS A 137 "
       model="  14" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.68e+00
  bond model="  14" pdb=" ND1 HIS A 137 "
       model="  14" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.67e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       97.19 -   103.51: 16
      103.51 -   109.84: 2001
      109.84 -   116.16: 986
      116.16 -   122.48: 750
      122.48 -   128.80: 326
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  14" pdb=" CA  HIS A  43 "
        model="  14" pdb=" CB  HIS A  43 "
        model="  14" pdb=" CG  HIS A  43 "
      ideal   model   delta    sigma   weight residual
     113.80  118.63   -4.83 1.00e+00 1.00e+00 2.33e+01
  angle model="  14" pdb=" OE1 GLN A  66 "
        model="  14" pdb=" CD  GLN A  66 "
        model="  14" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.79    4.81 1.00e+00 1.00e+00 2.32e+01
  angle model="  14" pdb=" CB  HIS A  43 "
        model="  14" pdb=" CG  HIS A  43 "
        model="  14" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  125.38    5.82 1.30e+00 5.92e-01 2.01e+01
  angle model="  14" pdb=" CB  HIS A 135 "
        model="  14" pdb=" CG  HIS A 135 "
        model="  14" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  125.42    5.78 1.30e+00 5.92e-01 1.98e+01
  angle model="  14" pdb=" C   HIS A 134 "
        model="  14" pdb=" CA  HIS A 134 "
        model="  14" pdb=" HA  HIS A 134 "
      ideal   model   delta    sigma   weight residual
     109.00   97.19   11.81 3.00e+00 1.11e-01 1.55e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.28: 908
       16.28 -    32.56: 85
       32.56 -    48.84: 25
       48.84 -    65.12: 7
       65.12 -    81.40: 8
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  14" pdb=" CA  GLU A 133 "
           model="  14" pdb=" C   GLU A 133 "
           model="  14" pdb=" N   HIS A 134 "
           model="  14" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.58  -39.42     0      5.00e+00 4.00e-02 6.22e+01
  dihedral model="  14" pdb=" CA  GLY A  42 "
           model="  14" pdb=" C   GLY A  42 "
           model="  14" pdb=" N   HIS A  43 "
           model="  14" pdb=" CA  HIS A  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.84  -24.16     0      5.00e+00 4.00e-02 2.33e+01
  dihedral model="  14" pdb=" CA  THR A  92 "
           model="  14" pdb=" C   THR A  92 "
           model="  14" pdb=" N   LEU A  93 "
           model="  14" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.51   23.49     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 122
       0.104 -    0.208: 46
       0.208 -    0.312: 5
       0.312 -    0.416: 2
       0.416 -    0.520: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  14" pdb=" CB  THR A  92 "
            model="  14" pdb=" CA  THR A  92 "
            model="  14" pdb=" OG1 THR A  92 "
            model="  14" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.03    0.52 2.00e-01 2.50e+01 6.77e+00
  chirality model="  14" pdb=" CA  HIS A 134 "
            model="  14" pdb=" N   HIS A 134 "
            model="  14" pdb=" C   HIS A 134 "
            model="  14" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.66e+00
  chirality model="  14" pdb=" CA  THR A  82 "
            model="  14" pdb=" N   THR A  82 "
            model="  14" pdb=" C   THR A  82 "
            model="  14" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.35 2.00e-01 2.50e+01 3.10e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  PHE A  15 "   -0.147 2.00e-02 2.50e+03   6.02e-02 1.09e+02
        model="  14" pdb=" CG  PHE A  15 "    0.015 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 PHE A  15 "    0.038 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 PHE A  15 "    0.032 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 PHE A  15 "    0.006 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 PHE A  15 "    0.011 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  PHE A  15 "   -0.034 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 PHE A  15 "    0.075 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 PHE A  15 "    0.057 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 PHE A  15 "    0.010 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 PHE A  15 "    0.027 2.00e-02 2.50e+03
        model="  14" pdb=" HZ  PHE A  15 "   -0.090 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  HIS A  43 "   -0.109 2.00e-02 2.50e+03   6.84e-02 9.36e+01
        model="  14" pdb=" CG  HIS A  43 "    0.064 2.00e-02 2.50e+03
        model="  14" pdb=" ND1 HIS A  43 "    0.120 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 HIS A  43 "    0.018 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 HIS A  43 "   -0.009 2.00e-02 2.50e+03
        model="  14" pdb=" NE2 HIS A  43 "   -0.032 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 HIS A  43 "    0.020 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 HIS A  43 "   -0.072 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  14" pdb=" CB  PHE A  67 "    0.069 2.00e-02 2.50e+03   5.30e-02 8.41e+01
        model="  14" pdb=" CG  PHE A  67 "   -0.043 2.00e-02 2.50e+03
        model="  14" pdb=" CD1 PHE A  67 "    0.006 2.00e-02 2.50e+03
        model="  14" pdb=" CD2 PHE A  67 "   -0.040 2.00e-02 2.50e+03
        model="  14" pdb=" CE1 PHE A  67 "   -0.032 2.00e-02 2.50e+03
        model="  14" pdb=" CE2 PHE A  67 "    0.015 2.00e-02 2.50e+03
        model="  14" pdb=" CZ  PHE A  67 "    0.020 2.00e-02 2.50e+03
        model="  14" pdb=" HD1 PHE A  67 "    0.064 2.00e-02 2.50e+03
        model="  14" pdb=" HD2 PHE A  67 "   -0.075 2.00e-02 2.50e+03
        model="  14" pdb=" HE1 PHE A  67 "   -0.091 2.00e-02 2.50e+03
        model="  14" pdb=" HE2 PHE A  67 "    0.048 2.00e-02 2.50e+03
        model="  14" pdb=" HZ  PHE A  67 "    0.059 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 140
        2.17 -     2.78: 4142
        2.78 -     3.39: 6026
        3.39 -     3.99: 7066
        3.99 -     4.60: 10682
  Nonbonded interactions: 28056
  Sorted by model distance:
  nonbonded model="  14" pdb="HG22 VAL A  57 "
            model="  14" pdb="HG22 ILE A 108 "
     model   vdw
     1.563 2.440
  nonbonded model="  14" pdb=" HB1 ALA A  60 "
            model="  14" pdb="HG12 VAL A 104 "
     model   vdw
     1.724 2.440
  nonbonded model="  14" pdb=" OD2 ASP A  44 "
            model="  14" pdb=" HG  SER A  46 "
     model   vdw
     1.788 1.850
  nonbonded model="  14" pdb=" OE2 GLU A  24 "
            model="  14" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.790 1.850
  nonbonded model="  14" pdb=" HZ2 LYS A  10 "
            model="  14" pdb=" OD1 ASP A  23 "
     model   vdw
     1.816 1.850
  ... (remaining 28051 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     9.83: 2224
        9.83 -    18.82: 0
       18.82 -    27.81: 0
       27.81 -    36.79: 0
       36.79 -    45.78: 1
  Warning: extremely large bond lengths.
  Bond restraints: 2225
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231 45.783 -44.552 2.00e-02 2.50e+03 4.96e+06
  bond model="   0" pdb=" N   SER A 130 "
       model="   0" pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.458  7.569 -6.111 1.90e-02 2.77e+03 1.03e+05
  bond model="   0" pdb=" CA  MET A 128 "
       model="   0" pdb=" C   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.525  7.773 -6.248 2.10e-02 2.27e+03 8.85e+04
  bond model="   0" pdb=" N   MET A 128 "
       model="   0" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  6.944 -5.486 1.90e-02 2.77e+03 8.34e+04
  bond model="   0" pdb=" CA  MET A 128 "
       model="   0" pdb=" CB  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.530  5.813 -4.283 2.00e-02 2.50e+03 4.59e+04
  ... (remaining 2220 not shown)

  Histogram of bond angle deviations from ideal:
        5.08 -    38.56: 7
       38.56 -    72.04: 20
       72.04 -   105.52: 238
      105.52 -   139.01: 3743
      139.01 -   172.49: 37
  Bond angle restraints: 4045
  Sorted by residual:
  angle model="   0" pdb=" C   MET A 128 "
        model="   0" pdb=" CA  MET A 128 "
        model="   0" pdb=" CB  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.10    5.08  105.02 1.90e+00 2.77e-01 3.06e+03
  angle model="   0" pdb=" C   TYR A  89 "
        model="   0" pdb=" N   SER A  90 "
        model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70   29.88   91.82 1.80e+00 3.09e-01 2.60e+03
  angle model="   0" pdb=" C   MET A 128 "
        model="   0" pdb=" N   ARG A 129 "
        model="   0" pdb=" CA  ARG A 129 "
      ideal   model   delta    sigma   weight residual
     121.70   32.97   88.73 1.80e+00 3.09e-01 2.43e+03
  angle model="   0" pdb=" CA  ALA A 124 "
        model="   0" pdb=" C   ALA A 124 "
        model="   0" pdb=" N   LYS A 125 "
      ideal   model   delta    sigma   weight residual
     116.20   20.55   95.65 2.00e+00 2.50e-01 2.29e+03
  angle model="   0" pdb=" N   MET A 128 "
        model="   0" pdb=" CA  MET A 128 "
        model="   0" pdb=" CB  MET A 128 "
      ideal   model   delta    sigma   weight residual
     110.50   32.07   78.43 1.70e+00 3.46e-01 2.13e+03
  ... (remaining 4040 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.76: 905
       23.76 -    47.52: 73
       47.52 -    71.28: 23
       71.28 -    95.04: 4
       95.04 -   118.80: 1
  Dihedral angle restraints: 1006
    sinusoidal: 548
      harmonic: 458
  Sorted by residual:
  dihedral model="   0" pdb=" C   MET A 128 "
           model="   0" pdb=" N   MET A 128 "
           model="   0" pdb=" CA  MET A 128 "
           model="   0" pdb=" CB  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60   -3.80 -118.80     0      2.50e+00 1.60e-01 2.26e+03
  dihedral model="   0" pdb=" N   VAL A 126 "
           model="   0" pdb=" C   VAL A 126 "
           model="   0" pdb=" CA  VAL A 126 "
           model="   0" pdb=" CB  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40   46.07   77.33     0      2.50e+00 1.60e-01 9.57e+02
  dihedral model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" C   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
           model="   0" pdb=" CB  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40   57.35   66.05     0      2.50e+00 1.60e-01 6.98e+02
  ... (remaining 1003 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    4.033: 169
       4.033 -    8.064: 6
       8.064 -   12.095: 0
      12.095 -   16.126: 0
      16.126 -   20.157: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A 130 "
            model="   0" pdb=" N   SER A 130 "
            model="   0" pdb=" C   SER A 130 "
            model="   0" pdb=" CB  SER A 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   22.67  -20.16 2.00e-01 2.50e+01 1.02e+04
  chirality model="   0" pdb=" CA  ALA A 124 "
            model="   0" pdb=" N   ALA A 124 "
            model="   0" pdb=" C   ALA A 124 "
            model="   0" pdb=" CB  ALA A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48   -5.11    7.59 2.00e-01 2.50e+01 1.44e+03
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -4.00    6.51 2.00e-01 2.50e+01 1.06e+03
  ... (remaining 173 not shown)

  Planarity restraints: 311
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.845 2.00e-02 2.50e+03   4.43e-01 5.88e+03
        model="   0" pdb=" CG  TYR A  89 "   -0.077 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.415 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.118 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.147 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.133 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.226 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.092 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.986 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.342 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.509 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  SER A 130 "    0.150 2.00e-02 2.50e+03   2.56e-01 6.56e+02
        model="   0" pdb=" C   SER A 130 "   -0.433 2.00e-02 2.50e+03
        model="   0" pdb=" O   SER A 130 "    0.219 2.00e-02 2.50e+03
        model="   0" pdb=" N   ILE A 131 "    0.063 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  LEU A  93 "   -0.112 2.00e-02 2.50e+03   1.95e-01 3.80e+02
        model="   0" pdb=" C   LEU A  93 "    0.329 2.00e-02 2.50e+03
        model="   0" pdb=" O   LEU A  93 "   -0.169 2.00e-02 2.50e+03
        model="   0" pdb=" N   GLY A  94 "   -0.048 2.00e-02 2.50e+03
  ... (remaining 308 not shown)

  Histogram of nonbonded interaction distances:
        0.45 -     1.28: 32
        1.28 -     2.11: 348
        2.11 -     2.94: 6155
        2.94 -     3.77: 9247
        3.77 -     4.60: 15206
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 30988
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   TYR A  89 "
            model="   0" pdb=" HA  SER A  90 "
     model   vdw
     0.453 2.620
  nonbonded model="   0" pdb=" C   GLY A 121 "
            model="   0" pdb=" HB  ILE A 122 "
     model   vdw
     0.717 2.920
  nonbonded model="   0" pdb=" HA  ILE A 122 "
            model="   0" pdb=" H   GLU A 123 "
     model   vdw
     0.748 2.270
  nonbonded model="   0" pdb=" C   LYS A 125 "
            model="   0" pdb=" HB  VAL A 126 "
     model   vdw
     0.833 2.920
  nonbonded model="   0" pdb=" HA  GLU A 123 "
            model="   0" pdb=" N   ALA A 124 "
     model   vdw
     0.849 2.216
  ... (remaining 30983 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CB  ILE A  78 "
        model="   6" pdb=" CB  LYS A  79 "
        model="   6" pdb=" CB  TYR A  89 "
        model="   6" pdb=" CB  ILE A 122 "
        model="   6" pdb=" CB  ALA A 124 "
        model="   6" pdb=" CB  HIS A 134 "
  Number of C-beta restraints generated:  250

  Time building geometry restraints manager: 1.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   8" pdb=" N   MET A   1 "
       model="   8" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.459  0.032 2.10e-02 2.27e+03 2.38e+00
  bond model="   8" pdb=" CZ  ARG A  58 "
       model="   8" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.92e-02
  bond model="   8" pdb=" CZ  ARG A  58 "
       model="   8" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.31e-02
  bond model="   8" pdb=" CZ  ARG A 129 "
       model="   8" pdb=" NH1 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.30e-02
  bond model="   8" pdb=" NE  ARG A 127 "
       model="   8" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.328 -0.002 1.10e-02 8.26e+03 5.11e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.88 -   106.88: 64
      106.88 -   112.89: 2721
      112.89 -   118.89: 426
      118.89 -   124.89: 824
      124.89 -   130.90: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   8" pdb=" CB  PRO A  52 "
        model="   8" pdb=" CA  PRO A  52 "
        model="   8" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.85   -4.85 3.00e+00 1.11e-01 2.61e+00
  angle model="   8" pdb=" CB  PRO A 114 "
        model="   8" pdb=" CA  PRO A 114 "
        model="   8" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.84   -4.84 3.00e+00 1.11e-01 2.60e+00
  angle model="   8" pdb=" CB  PRO A  54 "
        model="   8" pdb=" CA  PRO A  54 "
        model="   8" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   8" pdb=" CB  PRO A   6 "
        model="   8" pdb=" CA  PRO A   6 "
        model="   8" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   8" pdb=" CB  PRO A 117 "
        model="   8" pdb=" CA  PRO A 117 "
        model="   8" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 883
       17.05 -    34.10: 77
       34.10 -    51.15: 44
       51.15 -    68.19: 24
       68.19 -    85.24: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   8" pdb=" CB  GLU A 133 "
           model="   8" pdb=" CG  GLU A 133 "
           model="   8" pdb=" CD  GLU A 133 "
           model="   8" pdb=" OE1 GLU A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.24   85.24     1      3.00e+01 1.11e-03 9.78e+00
  dihedral model="   8" pdb=" CB  ARG A  58 "
           model="   8" pdb=" CG  ARG A  58 "
           model="   8" pdb=" CD  ARG A  58 "
           model="   8" pdb=" NE  ARG A  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.83  -59.17     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   8" pdb=" N   GLU A   8 "
           model="   8" pdb=" CA  GLU A   8 "
           model="   8" pdb=" CB  GLU A   8 "
           model="   8" pdb=" CG  GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.90   58.90     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 94
       0.019 -    0.038: 58
       0.038 -    0.057: 5
       0.057 -    0.076: 0
       0.076 -    0.095: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  ILE A  86 "
            model="   8" pdb=" N   ILE A  86 "
            model="   8" pdb=" C   ILE A  86 "
            model="   8" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.27e-01
  chirality model="   8" pdb=" CA  ILE A  38 "
            model="   8" pdb=" N   ILE A  38 "
            model="   8" pdb=" C   ILE A  38 "
            model="   8" pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.24e-01
  chirality model="   8" pdb=" CA  ILE A  71 "
            model="   8" pdb=" N   ILE A  71 "
            model="   8" pdb=" C   ILE A  71 "
            model="   8" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.19e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  PHE A  15 "   -0.001 2.00e-02 2.50e+03   1.50e-03 6.71e-02
        model="   8" pdb=" CG  PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 PHE A  15 "   -0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HZ  PHE A  15 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A 105 "   -0.001 2.00e-02 2.50e+03   1.15e-03 3.95e-02
        model="   8" pdb=" CG  TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A 105 "    0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A 105 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  TYR A  50 "    0.001 2.00e-02 2.50e+03   1.15e-03 3.94e-02
        model="   8" pdb=" CG  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" OH  TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 118
        2.12 -     2.74: 4194
        2.74 -     3.36: 5910
        3.36 -     3.98: 7045
        3.98 -     4.60: 10764
  Nonbonded interactions: 28031
  Sorted by model distance:
  nonbonded model="   8" pdb="HD23 LEU A   9 "
            model="   8" pdb="HD22 LEU A  26 "
     model   vdw
     1.502 2.440
  nonbonded model="   8" pdb="HG12 VAL A  41 "
            model="   8" pdb="HG22 VAL A 112 "
     model   vdw
     1.525 2.440
  nonbonded model="   8" pdb="HD11 LEU A  93 "
            model="   8" pdb="HD13 LEU A  99 "
     model   vdw
     1.646 2.440
  nonbonded model="   8" pdb="HG23 ILE A  37 "
            model="   8" pdb="HG21 ILE A 108 "
     model   vdw
     1.708 2.440
  nonbonded model="   8" pdb="HD11 ILE A   4 "
            model="   8" pdb="HG23 ILE A  30 "
     model   vdw
     1.726 2.440
  ... (remaining 28026 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 57
        1.23 -     1.43: 417
        1.43 -     1.62: 658
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   6" pdb=" N   LYS A 125 "
       model="   6" pdb=" CA  LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.554 -0.096 1.90e-02 2.77e+03 2.55e+01
  bond model="   6" pdb=" N   MET A 128 "
       model="   6" pdb=" CA  MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.458  1.552 -0.094 1.90e-02 2.77e+03 2.46e+01
  bond model="   6" pdb=" CA  SER A 130 "
       model="   6" pdb=" C   SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.525  1.620 -0.095 2.10e-02 2.27e+03 2.05e+01
  bond model="   6" pdb=" CA  GLY A  80 "
       model="   6" pdb=" C   GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.516  1.583 -0.067 1.80e-02 3.09e+03 1.38e+01
  bond model="   6" pdb=" CA  GLY A 121 "
       model="   6" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.582 -0.066 1.80e-02 3.09e+03 1.35e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       76.92 -    88.44: 4
       88.44 -    99.96: 18
       99.96 -   111.48: 2395
      111.48 -   122.99: 1404
      122.99 -   134.51: 258
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   6" pdb=" C   ILE A  78 "
        model="   6" pdb=" CA  ILE A  78 "
        model="   6" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   76.92   32.08 3.00e+00 1.11e-01 1.14e+02
  angle model="   6" pdb=" CB  ILE A  51 "
        model="   6" pdb=" CA  ILE A  51 "
        model="   6" pdb=" HA  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   79.05   29.95 3.00e+00 1.11e-01 9.96e+01
  angle model="   6" pdb=" CB  TYR A  81 "
        model="   6" pdb=" CA  TYR A  81 "
        model="   6" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     109.00   80.49   28.51 3.00e+00 1.11e-01 9.03e+01
  angle model="   6" pdb=" C   ILE A  51 "
        model="   6" pdb=" CA  ILE A  51 "
        model="   6" pdb=" HA  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   81.38   27.62 3.00e+00 1.11e-01 8.48e+01
  angle model="   6" pdb=" CA  ILE A 131 "
        model="   6" pdb=" CB  ILE A 131 "
        model="   6" pdb=" CG1 ILE A 131 "
      ideal   model   delta    sigma   weight residual
     110.40  124.80  -14.40 1.70e+00 3.46e-01 7.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.33: 952
       26.33 -    52.65: 53
       52.65 -    78.98: 9
       78.98 -   105.30: 3
      105.30 -   131.63: 2
  Dihedral angle restraints: 1019
    sinusoidal: 562
      harmonic: 457
  Sorted by residual:
  dihedral model="   6" pdb=" CA  LYS A  79 "
           model="   6" pdb=" C   LYS A  79 "
           model="   6" pdb=" N   GLY A  80 "
           model="   6" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   48.37  131.63     0      5.00e+00 4.00e-02 6.93e+02
  dihedral model="   6" pdb=" CA  ILE A 122 "
           model="   6" pdb=" C   ILE A 122 "
           model="   6" pdb=" N   GLU A 123 "
           model="   6" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   69.12  110.88     0      5.00e+00 4.00e-02 4.92e+02
  dihedral model="   6" pdb=" C   TYR A  81 "
           model="   6" pdb=" N   TYR A  81 "
           model="   6" pdb=" CA  TYR A  81 "
           model="   6" pdb=" CB  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -171.82   49.22     0      2.50e+00 1.60e-01 3.88e+02
  ... (remaining 1016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.112: 165
       1.112 -    2.224: 1
       2.224 -    3.336: 2
       3.336 -    4.448: 2
       4.448 -    5.560: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   6" pdb=" CA  LYS A  79 "
            model="   6" pdb=" N   LYS A  79 "
            model="   6" pdb=" C   LYS A  79 "
            model="   6" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.05    5.56 2.00e-01 2.50e+01 7.73e+02
  chirality model="   6" pdb=" CB  ILE A 131 "
            model="   6" pdb=" CA  ILE A 131 "
            model="   6" pdb=" CG1 ILE A 131 "
            model="   6" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.77    5.41 2.00e-01 2.50e+01 7.32e+02
  chirality model="   6" pdb=" CB  ILE A  78 "
            model="   6" pdb=" CA  ILE A  78 "
            model="   6" pdb=" CG1 ILE A  78 "
            model="   6" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.41    5.05 2.00e-01 2.50e+01 6.38e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A  50 "   -0.209 2.00e-02 2.50e+03   8.89e-02 2.37e+02
        model="   6" pdb=" CG  TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A  50 "    0.044 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A  50 "    0.044 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A  50 "    0.029 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A  50 "   -0.176 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A  50 "    0.071 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A  50 "    0.070 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A  50 "    0.046 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A  50 "    0.047 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CA  SER A 130 "    0.042 2.00e-02 2.50e+03   8.32e-02 6.93e+01
        model="   6" pdb=" C   SER A 130 "   -0.144 2.00e-02 2.50e+03
        model="   6" pdb=" O   SER A 130 "    0.054 2.00e-02 2.50e+03
        model="   6" pdb=" N   ILE A 131 "    0.047 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   6" pdb=" CB  TYR A 105 "    0.117 2.00e-02 2.50e+03   4.65e-02 6.47e+01
        model="   6" pdb=" CG  TYR A 105 "   -0.028 2.00e-02 2.50e+03
        model="   6" pdb=" CD1 TYR A 105 "   -0.025 2.00e-02 2.50e+03
        model="   6" pdb=" CD2 TYR A 105 "   -0.028 2.00e-02 2.50e+03
        model="   6" pdb=" CE1 TYR A 105 "   -0.013 2.00e-02 2.50e+03
        model="   6" pdb=" CE2 TYR A 105 "   -0.010 2.00e-02 2.50e+03
        model="   6" pdb=" CZ  TYR A 105 "    0.008 2.00e-02 2.50e+03
        model="   6" pdb=" OH  TYR A 105 "    0.081 2.00e-02 2.50e+03
        model="   6" pdb=" HD1 TYR A 105 "   -0.031 2.00e-02 2.50e+03
        model="   6" pdb=" HD2 TYR A 105 "   -0.040 2.00e-02 2.50e+03
        model="   6" pdb=" HE1 TYR A 105 "   -0.019 2.00e-02 2.50e+03
        model="   6" pdb=" HE2 TYR A 105 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.10: 82
        2.10 -     2.72: 3596
        2.72 -     3.35: 6605
        3.35 -     3.97: 7986
        3.97 -     4.60: 12027
  Nonbonded interactions: 30296
  Sorted by model distance:
  nonbonded model="   6" pdb=" H   TYR A  81 "
            model="   6" pdb="HG21 THR A  92 "
     model   vdw
     1.469 2.270
  nonbonded model="   6" pdb=" HA  ALA A 124 "
            model="   6" pdb=" H   VAL A 126 "
     model   vdw
     1.545 2.270
  nonbonded model="   6" pdb=" HA  ILE A  51 "
            model="   6" pdb=" HB  ILE A  51 "
     model   vdw
     1.666 1.952
  nonbonded model="   6" pdb=" HA  SER A 130 "
            model="   6" pdb="HG23 ILE A 131 "
     model   vdw
     1.719 2.440
  nonbonded model="   6" pdb="HG13 ILE A 131 "
            model="   6" pdb=" H   LEU A 132 "
     model   vdw
     1.757 2.270
  ... (remaining 30291 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 0.78, per 1000 atoms: 0.35
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.112, 54.167, 47.612, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.194, 60.984, 58.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A LEU   31": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A VAL  112": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   8"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.04, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (64.029, 45.272, 53.402, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.597, 44.335, 67.481, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  13" pdb=" CB  ASP A  44 "
        model="  13" pdb=" CB  SER A  90 "
        model="  13" pdb=" CB  LYS A 113 "
        model="  13" pdb=" CB  ARG A 129 "
  Number of C-beta restraints generated:  256

  Time building geometry restraints manager: 1.09 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.45e+00
  bond model="   9" pdb=" NE  ARG A  21 "
       model="   9" pdb=" CZ  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 8.68e-02
  bond model="   9" pdb=" CZ  ARG A  21 "
       model="   9" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.326  0.004 1.30e-02 5.92e+03 8.39e-02
  bond model="   9" pdb=" NE  ARG A  58 "
       model="   9" pdb=" CZ  ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 6.80e-02
  bond model="   9" pdb=" CZ  ARG A  58 "
       model="   9" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.77e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.89 -   106.89: 65
      106.89 -   112.89: 2720
      112.89 -   118.89: 426
      118.89 -   124.89: 824
      124.89 -   130.89: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A 102 "
        model="   9" pdb=" CA  PRO A 102 "
        model="   9" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.87   -4.87 3.00e+00 1.11e-01 2.64e+00
  angle model="   9" pdb=" CB  PRO A  54 "
        model="   9" pdb=" CA  PRO A  54 "
        model="   9" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   9" pdb=" CB  PRO A   6 "
        model="   9" pdb=" CA  PRO A   6 "
        model="   9" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A 117 "
        model="   9" pdb=" CA  PRO A 117 "
        model="   9" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A 114 "
        model="   9" pdb=" CA  PRO A 114 "
        model="   9" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 892
       17.69 -    35.37: 76
       35.37 -    53.06: 41
       53.06 -    70.75: 17
       70.75 -    88.43: 6
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CB  GLU A   8 "
           model="   9" pdb=" CG  GLU A   8 "
           model="   9" pdb=" CD  GLU A   8 "
           model="   9" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.43   88.43     1      3.00e+01 1.11e-03 1.04e+01
  dihedral model="   9" pdb=" CB  GLU A 133 "
           model="   9" pdb=" CG  GLU A 133 "
           model="   9" pdb=" CD  GLU A 133 "
           model="   9" pdb=" OE1 GLU A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.62  -87.62     1      3.00e+01 1.11e-03 1.02e+01
  dihedral model="   9" pdb=" CB  GLU A  55 "
           model="   9" pdb=" CG  GLU A  55 "
           model="   9" pdb=" CD  GLU A  55 "
           model="   9" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.59   86.59     1      3.00e+01 1.11e-03 1.00e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 102
       0.019 -    0.038: 54
       0.038 -    0.058: 1
       0.058 -    0.077: 0
       0.077 -    0.096: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A  86 "
            model="   9" pdb=" N   ILE A  86 "
            model="   9" pdb=" C   ILE A  86 "
            model="   9" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.30e-01
  chirality model="   9" pdb=" CA  ILE A  38 "
            model="   9" pdb=" N   ILE A  38 "
            model="   9" pdb=" C   ILE A  38 "
            model="   9" pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.22e-01
  chirality model="   9" pdb=" CA  ILE A 131 "
            model="   9" pdb=" N   ILE A 131 "
            model="   9" pdb=" C   ILE A 131 "
            model="   9" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.21e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  91 "   -0.000 2.00e-02 2.50e+03   1.40e-03 5.89e-02
        model="   9" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  91 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  45 "    0.000 2.00e-02 2.50e+03   1.38e-03 5.70e-02
        model="   9" pdb=" CG  PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  45 "    0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  45 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A 111 "    0.000 2.00e-02 2.50e+03   1.16e-03 4.05e-02
        model="   9" pdb=" CG  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 104
        2.09 -     2.72: 4002
        2.72 -     3.34: 6126
        3.34 -     3.97: 7372
        3.97 -     4.60: 11342
  Nonbonded interactions: 28946
  Sorted by model distance:
  nonbonded model="   9" pdb="HD23 LEU A   9 "
            model="   9" pdb="HD22 LEU A  26 "
     model   vdw
     1.462 2.440
  nonbonded model="   9" pdb="HD11 LEU A  93 "
            model="   9" pdb="HD13 LEU A  99 "
     model   vdw
     1.627 2.440
  nonbonded model="   9" pdb="HG12 VAL A  41 "
            model="   9" pdb="HG22 VAL A 112 "
     model   vdw
     1.638 2.440
  nonbonded model="   9" pdb="HG23 ILE A  37 "
            model="   9" pdb="HD13 ILE A 108 "
     model   vdw
     1.654 2.440
  nonbonded model="   9" pdb="HG23 VAL A  41 "
            model="   9" pdb=" H   HIS A  43 "
     model   vdw
     1.726 2.270
  ... (remaining 28941 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (75.117, 69.978, 41.746, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 75
        1.23 -     1.42: 396
        1.42 -     1.62: 661
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  13" pdb=" CD2 HIS A 138 "
       model="  13" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.78e+00
  bond model="  13" pdb=" CZ  ARG A  21 "
       model="  13" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.21e+00
  bond model="  13" pdb=" CD2 HIS A 139 "
       model="  13" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.94e+00
  bond model="  13" pdb=" CZ  ARG A  58 "
       model="  13" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.68e+00
  bond model="  13" pdb=" CD2 HIS A 137 "
       model="  13" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.49e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       91.77 -   100.02: 8
      100.02 -   108.27: 620
      108.27 -   116.51: 2382
      116.51 -   124.76: 990
      124.76 -   133.01: 79
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  13" pdb=" C   MET A 128 "
        model="  13" pdb=" N   ARG A 129 "
        model="  13" pdb=" CA  ARG A 129 "
      ideal   model   delta    sigma   weight residual
     121.70  133.01  -11.31 1.80e+00 3.09e-01 3.95e+01
  angle model="  13" pdb=" C   VAL A 112 "
        model="  13" pdb=" N   LYS A 113 "
        model="  13" pdb=" CA  LYS A 113 "
      ideal   model   delta    sigma   weight residual
     121.70  132.46  -10.76 1.80e+00 3.09e-01 3.57e+01
  angle model="  13" pdb=" C   LYS A 113 "
        model="  13" pdb=" CA  LYS A 113 "
        model="  13" pdb=" HA  LYS A 113 "
      ideal   model   delta    sigma   weight residual
     109.00   91.77   17.23 3.00e+00 1.11e-01 3.30e+01
  angle model="  13" pdb=" CA  HIS A 138 "
        model="  13" pdb=" CB  HIS A 138 "
        model="  13" pdb=" CG  HIS A 138 "
      ideal   model   delta    sigma   weight residual
     113.80  118.78   -4.98 1.00e+00 1.00e+00 2.48e+01
  angle model="  13" pdb=" C   HIS A  43 "
        model="  13" pdb=" N   ASP A  44 "
        model="  13" pdb=" CA  ASP A  44 "
      ideal   model   delta    sigma   weight residual
     121.70  129.92   -8.22 1.80e+00 3.09e-01 2.08e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 937
       17.45 -    34.91: 52
       34.91 -    52.36: 23
       52.36 -    69.81: 5
       69.81 -    87.26: 8
  Dihedral angle restraints: 1025
    sinusoidal: 562
      harmonic: 463
  Sorted by residual:
  dihedral model="  13" pdb=" CA  ARG A 129 "
           model="  13" pdb=" C   ARG A 129 "
           model="  13" pdb=" N   SER A 130 "
           model="  13" pdb=" CA  SER A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.30  -44.70     0      5.00e+00 4.00e-02 7.99e+01
  dihedral model="  13" pdb=" CA  ASP A  44 "
           model="  13" pdb=" C   ASP A  44 "
           model="  13" pdb=" N   PHE A  45 "
           model="  13" pdb=" CA  PHE A  45 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.86  -32.14     0      5.00e+00 4.00e-02 4.13e+01
  dihedral model="  13" pdb=" N   MET A 128 "
           model="  13" pdb=" C   MET A 128 "
           model="  13" pdb=" CA  MET A 128 "
           model="  13" pdb=" CB  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.09  -13.29     0      2.50e+00 1.60e-01 2.82e+01
  ... (remaining 1022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.912: 172
       0.912 -    1.823: 0
       1.823 -    2.734: 0
       2.734 -    3.645: 0
       3.645 -    4.556: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  13" pdb=" CA  SER A  90 "
            model="  13" pdb=" N   SER A  90 "
            model="  13" pdb=" C   SER A  90 "
            model="  13" pdb=" CB  SER A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.05    4.56 2.00e-01 2.50e+01 5.19e+02
  chirality model="  13" pdb=" CA  ARG A 129 "
            model="  13" pdb=" N   ARG A 129 "
            model="  13" pdb=" C   ARG A 129 "
            model="  13" pdb=" CB  ARG A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.93    4.44 2.00e-01 2.50e+01 4.92e+02
  chirality model="  13" pdb=" CA  ASP A  44 "
            model="  13" pdb=" N   ASP A  44 "
            model="  13" pdb=" C   ASP A  44 "
            model="  13" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.66    4.17 2.00e-01 2.50e+01 4.34e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  91 "    0.320 2.00e-02 2.50e+03   1.34e-01 5.42e+02
        model="  13" pdb=" CG  TYR A  91 "   -0.050 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  91 "   -0.045 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  91 "   -0.110 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  91 "   -0.042 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  91 "    0.023 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  91 "    0.027 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  91 "    0.132 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  91 "   -0.044 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  91 "   -0.237 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  91 "   -0.084 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  91 "    0.110 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A  89 "   -0.136 2.00e-02 2.50e+03   9.24e-02 2.56e+02
        model="  13" pdb=" CG  TYR A  89 "   -0.071 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A  89 "    0.056 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A  89 "    0.047 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A  89 "   -0.016 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A  89 "   -0.041 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A  89 "   -0.116 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A  89 "    0.190 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A  89 "    0.142 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A  89 "   -0.045 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  13" pdb=" CB  TYR A 111 "   -0.092 2.00e-02 2.50e+03   5.55e-02 9.23e+01
        model="  13" pdb=" CG  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="  13" pdb=" CD1 TYR A 111 "    0.026 2.00e-02 2.50e+03
        model="  13" pdb=" CD2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="  13" pdb=" CE1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="  13" pdb=" CE2 TYR A 111 "    0.037 2.00e-02 2.50e+03
        model="  13" pdb=" CZ  TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="  13" pdb=" OH  TYR A 111 "   -0.129 2.00e-02 2.50e+03
        model="  13" pdb=" HD1 TYR A 111 "    0.054 2.00e-02 2.50e+03
        model="  13" pdb=" HD2 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="  13" pdb=" HE1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="  13" pdb=" HE2 TYR A 111 "    0.079 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 113
        2.14 -     2.76: 3902
        2.76 -     3.37: 6010
        3.37 -     3.99: 7156
        3.99 -     4.60: 10828
  Nonbonded interactions: 28009
  Sorted by model distance:
  nonbonded model="  13" pdb="HG23 VAL A  41 "
            model="  13" pdb=" H   HIS A  43 "
     model   vdw
     1.528 2.270
  nonbonded model="  13" pdb=" OD2 ASP A  36 "
            model="  13" pdb=" HZ2 LYS A  40 "
     model   vdw
     1.797 1.850
  nonbonded model="  13" pdb=" OD1 ASP A  44 "
            model="  13" pdb=" HG  SER A  46 "
     model   vdw
     1.810 1.850
  nonbonded model="  13" pdb=" HZ3 LYS A  63 "
            model="  13" pdb=" OD2 ASP A  88 "
     model   vdw
     1.845 1.850
  nonbonded model="  13" pdb=" OE1 GLU A  24 "
            model="  13" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.860 1.850
  ... (remaining 28004 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.09 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  ASP A  74 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" CB  LYS A  79 "
        model="   4" pdb=" CB  THR A  92 "
        model="   4" pdb=" CB  SER A  98 "
        model="   4" pdb=" CB  GLU A 123 "
        model="   4" pdb=" CB  ILE A 131 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 0.76 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 70
        1.23 -     1.42: 402
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  11" pdb=" CD2 HIS A 139 "
       model="  11" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.406 -0.032 1.10e-02 8.26e+03 8.37e+00
  bond model="  11" pdb=" CZ  ARG A  21 "
       model="  11" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 7.91e+00
  bond model="  11" pdb=" CD2 HIS A 137 "
       model="  11" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.47e+00
  bond model="  11" pdb=" CZ  ARG A  58 "
       model="  11" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.15e+00
  bond model="  11" pdb=" CD2 HIS A 138 "
       model="  11" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.06e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.98 -   106.97: 233
      106.97 -   112.95: 2488
      112.95 -   118.93: 488
      118.93 -   124.91: 805
      124.91 -   130.89: 65
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  11" pdb=" OE1 GLN A  66 "
        model="  11" pdb=" CD  GLN A  66 "
        model="  11" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.75    4.85 1.00e+00 1.00e+00 2.35e+01
  angle model="  11" pdb=" OE1 GLN A  28 "
        model="  11" pdb=" CD  GLN A  28 "
        model="  11" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.47    4.13 1.00e+00 1.00e+00 1.71e+01
  angle model="  11" pdb=" CA  LYS A 109 "
        model="  11" pdb=" CB  LYS A 109 "
        model="  11" pdb=" CG  LYS A 109 "
      ideal   model   delta    sigma   weight residual
     114.10  106.87    7.23 2.00e+00 2.50e-01 1.31e+01
  angle model="  11" pdb=" CA  ASN A  72 "
        model="  11" pdb=" CB  ASN A  72 "
        model="  11" pdb=" CG  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     112.60  116.19   -3.59 1.00e+00 1.00e+00 1.29e+01
  angle model="  11" pdb=" N   PRO A 114 "
        model="  11" pdb=" CA  PRO A 114 "
        model="  11" pdb=" CB  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     103.00  106.88   -3.88 1.10e+00 8.26e-01 1.24e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 926
       17.83 -    35.65: 70
       35.65 -    53.48: 23
       53.48 -    71.31: 6
       71.31 -    89.14: 8
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  11" pdb=" CA  LEU A   2 "
           model="  11" pdb=" C   LEU A   2 "
           model="  11" pdb=" N   LEU A   3 "
           model="  11" pdb=" CA  LEU A   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.03  -29.97     0      5.00e+00 4.00e-02 3.59e+01
  dihedral model="  11" pdb=" CA  VAL A 112 "
           model="  11" pdb=" C   VAL A 112 "
           model="  11" pdb=" N   LYS A 113 "
           model="  11" pdb=" CA  LYS A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.89   29.11     0      5.00e+00 4.00e-02 3.39e+01
  dihedral model="  11" pdb=" C   LEU A   3 "
           model="  11" pdb=" N   LEU A   3 "
           model="  11" pdb=" CA  LEU A   3 "
           model="  11" pdb=" CB  LEU A   3 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.57    9.97     0      2.50e+00 1.60e-01 1.59e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 105
       0.085 -    0.169: 61
       0.169 -    0.254: 8
       0.254 -    0.338: 0
       0.338 -    0.422: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  11" pdb=" CA  LEU A   3 "
            model="  11" pdb=" N   LEU A   3 "
            model="  11" pdb=" C   LEU A   3 "
            model="  11" pdb=" CB  LEU A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.46e+00
  chirality model="  11" pdb=" CA  LYS A 109 "
            model="  11" pdb=" N   LYS A 109 "
            model="  11" pdb=" C   LYS A 109 "
            model="  11" pdb=" CB  LYS A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.65e+00
  chirality model="  11" pdb=" CG  LEU A   3 "
            model="  11" pdb=" CB  LEU A   3 "
            model="  11" pdb=" CD1 LEU A   3 "
            model="  11" pdb=" CD2 LEU A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  12 "    0.121 2.00e-02 2.50e+03   5.48e-02 9.00e+01
        model="  11" pdb=" CG  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  12 "   -0.025 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  12 "   -0.023 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  12 "    0.115 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  12 "   -0.047 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  12 "   -0.043 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  12 "   -0.031 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  12 "   -0.036 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  68 "    0.123 2.00e-02 2.50e+03   5.04e-02 7.61e+01
        model="  11" pdb=" CG  TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  68 "   -0.032 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  68 "   -0.023 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  68 "   -0.004 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  68 "   -0.011 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  68 "    0.028 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  68 "    0.071 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  68 "   -0.070 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  68 "   -0.046 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  68 "   -0.007 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  68 "   -0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  11" pdb=" CB  TYR A  50 "   -0.097 2.00e-02 2.50e+03   3.91e-02 4.59e+01
        model="  11" pdb=" CG  TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="  11" pdb=" CD1 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="  11" pdb=" CD2 TYR A  50 "    0.026 2.00e-02 2.50e+03
        model="  11" pdb=" CE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="  11" pdb=" CE2 TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="  11" pdb=" CZ  TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="  11" pdb=" OH  TYR A  50 "   -0.065 2.00e-02 2.50e+03
        model="  11" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="  11" pdb=" HD2 TYR A  50 "    0.043 2.00e-02 2.50e+03
        model="  11" pdb=" HE1 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="  11" pdb=" HE2 TYR A  50 "    0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.35: 606
        2.35 -     2.92: 5082
        2.92 -     3.48: 5205
        3.48 -     4.04: 6640
        4.04 -     4.60: 9873
  Nonbonded interactions: 27406
  Sorted by model distance:
  nonbonded model="  11" pdb=" HG1 THR A   5 "
            model="  11" pdb=" OE2 GLU A   8 "
     model   vdw
     1.793 1.850
  nonbonded model="  11" pdb=" OE2 GLU A 123 "
            model="  11" pdb=" HZ1 LYS A 125 "
     model   vdw
     1.803 1.850
  nonbonded model="  11" pdb=" HE1 TYR A  50 "
            model="  11" pdb="HG11 VAL A 112 "
     model   vdw
     1.805 2.270
  nonbonded model="  11" pdb="HG23 VAL A  41 "
            model="  11" pdb=" H   HIS A  43 "
     model   vdw
     1.843 2.270
  nonbonded model="  11" pdb=" O   ILE A  30 "
            model="  11" pdb=" HG1 THR A  34 "
     model   vdw
     1.866 1.850
  ... (remaining 27401 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 61
        1.23 -     1.43: 412
        1.43 -     1.62: 656
        1.62 -     1.82: 7
  Bond restraints: 2242
  Sorted by residual:
  bond model="   4" pdb=" C   ILE A  78 "
       model="   4" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.463 -0.134 1.40e-02 5.10e+03 9.14e+01
  bond model="   4" pdb=" CB  ILE A  78 "
       model="   4" pdb=" CG1 ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.530  1.712 -0.182 2.00e-02 2.50e+03 8.32e+01
  bond model="   4" pdb=" CA  ILE A  78 "
       model="   4" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.656 -0.131 2.10e-02 2.27e+03 3.90e+01
  bond model="   4" pdb=" N   LYS A  79 "
       model="   4" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.567 -0.109 1.90e-02 2.77e+03 3.32e+01
  bond model="   4" pdb=" N   ILE A  77 "
       model="   4" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.542 -0.084 1.90e-02 2.77e+03 1.94e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       57.61 -    77.87: 3
       77.87 -    98.13: 17
       98.13 -   118.39: 3110
      118.39 -   138.64: 946
      138.64 -   158.90: 3
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   4" pdb=" CB  TYR A  89 "
        model="   4" pdb=" CA  TYR A  89 "
        model="   4" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   57.61   51.39 3.00e+00 1.11e-01 2.93e+02
  angle model="   4" pdb=" N   TYR A  89 "
        model="   4" pdb=" CA  TYR A  89 "
        model="   4" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.00  158.90  -48.90 3.00e+00 1.11e-01 2.66e+02
  angle model="   4" pdb=" CG2 ILE A  78 "
        model="   4" pdb=" CB  ILE A  78 "
        model="   4" pdb=" HB  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   71.87   37.13 3.00e+00 1.11e-01 1.53e+02
  angle model="   4" pdb=" N   LYS A  79 "
        model="   4" pdb=" CA  LYS A  79 "
        model="   4" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.50   90.51   19.99 1.70e+00 3.46e-01 1.38e+02
  angle model="   4" pdb=" C   TYR A  89 "
        model="   4" pdb=" CA  TYR A  89 "
        model="   4" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   76.32   32.68 3.00e+00 1.11e-01 1.19e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.93: 952
       24.93 -    49.86: 46
       49.86 -    74.79: 11
       74.79 -    99.71: 6
       99.71 -   124.64: 2
  Dihedral angle restraints: 1017
    sinusoidal: 562
      harmonic: 455
  Sorted by residual:
  dihedral model="   4" pdb=" CA  GLY A  80 "
           model="   4" pdb=" C   GLY A  80 "
           model="   4" pdb=" N   TYR A  81 "
           model="   4" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   55.36  124.64     0      5.00e+00 4.00e-02 6.21e+02
  dihedral model="   4" pdb=" CA  TYR A  89 "
           model="   4" pdb=" C   TYR A  89 "
           model="   4" pdb=" N   SER A  90 "
           model="   4" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -68.53 -111.47     0      5.00e+00 4.00e-02 4.97e+02
  dihedral model="   4" pdb=" C   TYR A  89 "
           model="   4" pdb=" N   TYR A  89 "
           model="   4" pdb=" CA  TYR A  89 "
           model="   4" pdb=" CB  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -176.62   54.02     0      2.50e+00 1.60e-01 4.67e+02
  ... (remaining 1014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.204: 165
       1.204 -    2.407: 1
       2.407 -    3.610: 2
       3.610 -    4.813: 1
       4.813 -    6.017: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CA  LYS A  79 "
            model="   4" pdb=" N   LYS A  79 "
            model="   4" pdb=" C   LYS A  79 "
            model="   4" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.51    6.02 2.00e-01 2.50e+01 9.05e+02
  chirality model="   4" pdb=" CA  THR A  92 "
            model="   4" pdb=" N   THR A  92 "
            model="   4" pdb=" C   THR A  92 "
            model="   4" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.88    5.40 2.00e-01 2.50e+01 7.29e+02
  chirality model="   4" pdb=" CB  ILE A 131 "
            model="   4" pdb=" CA  ILE A 131 "
            model="   4" pdb=" CG1 ILE A 131 "
            model="   4" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.69    5.33 2.00e-01 2.50e+01 7.10e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  89 "   -0.217 2.00e-02 2.50e+03   9.86e-02 2.92e+02
        model="   4" pdb=" CG  TYR A  89 "   -0.048 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  89 "    0.055 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  89 "    0.034 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  89 "    0.030 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  89 "   -0.036 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  89 "   -0.154 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  89 "    0.154 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  89 "    0.091 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  89 "    0.070 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A 111 "    0.159 2.00e-02 2.50e+03   6.15e-02 1.13e+02
        model="   4" pdb=" CG  TYR A 111 "   -0.030 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A 111 "   -0.033 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A 111 "   -0.041 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A 111 "    0.088 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A 111 "   -0.047 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A 111 "   -0.073 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  12 "    0.110 2.00e-02 2.50e+03   4.95e-02 7.34e+01
        model="   4" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  12 "   -0.025 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  12 "    0.103 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  12 "   -0.044 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  12 "   -0.029 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  12 "   -0.025 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  12 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.36 -     2.01: 55
        2.01 -     2.65: 2888
        2.65 -     3.30: 6910
        3.30 -     3.95: 8167
        3.95 -     4.60: 12322
  Nonbonded interactions: 30342
  Sorted by model distance:
  nonbonded model="   4" pdb=" HA  TYR A  89 "
            model="   4" pdb=" HB3 TYR A  89 "
     model   vdw
     1.357 1.952
  nonbonded model="   4" pdb=" HB3 LYS A  79 "
            model="   4" pdb=" HA  THR A  82 "
     model   vdw
     1.658 2.440
  nonbonded model="   4" pdb=" HA  THR A  92 "
            model="   4" pdb=" HA  SER A  98 "
     model   vdw
     1.704 2.440
  nonbonded model="   4" pdb=" H   ASP A  74 "
            model="   4" pdb=" H   SER A  76 "
     model   vdw
     1.718 2.100
  nonbonded model="   4" pdb=" OD1 ASP A  44 "
            model="   4" pdb=" HG  SER A  46 "
     model   vdw
     1.732 1.850
  ... (remaining 30337 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.71, per 1000 atoms: 0.32
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.164, 44.245, 58.735, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 130}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   7"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.552, 55.633, 51.111, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  12" pdb=" CB  ASN A  72 "
  Number of C-beta restraints generated:  262

  Time building geometry restraints manager: 0.75 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 125
        1.23 -     1.43: 347
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" CZ  ARG A  58 "
       model="  12" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.79e+00
  bond model="  12" pdb=" CD2 HIS A 137 "
       model="  12" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.61e+00
  bond model="  12" pdb=" CZ  ARG A  21 "
       model="  12" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.25e+00
  bond model="  12" pdb=" CD2 HIS A 135 "
       model="  12" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.22e+00
  bond model="  12" pdb=" CD2 HIS A 139 "
       model="  12" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.54e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       93.42 -   101.01: 4
      101.01 -   108.59: 726
      108.59 -   116.17: 2261
      116.17 -   123.76: 957
      123.76 -   131.34: 131
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" C   ILE A  71 "
        model="  12" pdb=" N   ASN A  72 "
        model="  12" pdb=" CA  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     121.70  131.34   -9.64 1.80e+00 3.09e-01 2.87e+01
  angle model="  12" pdb=" C   ASN A  72 "
        model="  12" pdb=" CA  ASN A  72 "
        model="  12" pdb=" HA  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     109.00   93.42   15.58 3.00e+00 1.11e-01 2.70e+01
  angle model="  12" pdb=" CB  HIS A 136 "
        model="  12" pdb=" CG  HIS A 136 "
        model="  12" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  124.90    6.30 1.30e+00 5.92e-01 2.35e+01
  angle model="  12" pdb=" CA  ASP A  74 "
        model="  12" pdb=" C   ASP A  74 "
        model="  12" pdb=" O   ASP A  74 "
      ideal   model   delta    sigma   weight residual
     120.80  128.99   -8.19 1.70e+00 3.46e-01 2.32e+01
  angle model="  12" pdb=" CA  ASN A  72 "
        model="  12" pdb=" CB  ASN A  72 "
        model="  12" pdb=" CG  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     112.60  117.23   -4.63 1.00e+00 1.00e+00 2.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.39: 955
       21.39 -    42.79: 60
       42.79 -    64.18: 12
       64.18 -    85.58: 3
       85.58 -   106.97: 1
  Dihedral angle restraints: 1031
    sinusoidal: 562
      harmonic: 469
  Sorted by residual:
  dihedral model="  12" pdb=" CA  GLY A  73 "
           model="  12" pdb=" C   GLY A  73 "
           model="  12" pdb=" N   ASP A  74 "
           model="  12" pdb=" CA  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -73.03 -106.97     0      5.00e+00 4.00e-02 4.58e+02
  dihedral model="  12" pdb=" CA  ASP A  88 "
           model="  12" pdb=" C   ASP A  88 "
           model="  12" pdb=" N   TYR A  89 "
           model="  12" pdb=" CA  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -121.77  -58.23     0      5.00e+00 4.00e-02 1.36e+02
  dihedral model="  12" pdb=" CA  ILE A  71 "
           model="  12" pdb=" C   ILE A  71 "
           model="  12" pdb=" N   ASN A  72 "
           model="  12" pdb=" CA  ASN A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.06  -49.94     0      5.00e+00 4.00e-02 9.98e+01
  ... (remaining 1028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.852: 175
       0.852 -    1.703: 0
       1.703 -    2.555: 0
       2.555 -    3.406: 0
       
  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   0" pdb=" CB  ILE A  51 "
        model="   0" pdb=" CB  ILE A  78 "
        model="   0" pdb=" CB  LYS A  79 "
        model="   0" pdb=" CB  THR A  92 "
        model="   0" pdb=" CB  LEU A  93 "
        model="   0" pdb=" CB  SER A  97 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.24 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.048, 60.381, 58.536, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
3.406 -    4.257: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  ASN A  72 "
            model="  12" pdb=" N   ASN A  72 "
            model="  12" pdb=" C   ASN A  72 "
            model="  12" pdb=" CB  ASN A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.75    4.26 2.00e-01 2.50e+01 4.53e+02
  chirality model="  12" pdb=" CA  ASP A  74 "
            model="  12" pdb=" N   ASP A  74 "
            model="  12" pdb=" C   ASP A  74 "
            model="  12" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.95e+00
  chirality model="  12" pdb=" CA  MET A 128 "
            model="  12" pdb=" N   MET A 128 "
            model="  12" pdb=" C   MET A 128 "
            model="  12" pdb=" CB  MET A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  HIS A 136 "   -0.160 2.00e-02 2.50e+03   9.48e-02 1.80e+02
        model="  12" pdb=" CG  HIS A 136 "    0.132 2.00e-02 2.50e+03
        model="  12" pdb=" ND1 HIS A 136 "    0.133 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 HIS A 136 "    0.030 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 HIS A 136 "   -0.015 2.00e-02 2.50e+03
        model="  12" pdb=" NE2 HIS A 136 "   -0.056 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 HIS A 136 "    0.019 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 HIS A 136 "   -0.081 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A 111 "   -0.193 2.00e-02 2.50e+03   7.71e-02 1.78e+02
        model="  12" pdb=" CG  TYR A 111 "    0.071 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A 111 "    0.035 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A 111 "    0.066 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A 111 "   -0.059 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A 111 "    0.114 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A 111 "   -0.076 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A 105 "   -0.124 2.00e-02 2.50e+03   7.42e-02 1.65e+02
        model="  12" pdb=" CG  TYR A 105 "    0.015 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A 105 "    0.051 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A 105 "   -0.002 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A 105 "   -0.004 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A 105 "    0.048 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A 105 "   -0.007 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A 105 "   -0.123 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A 105 "    0.112 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A 105 "   -0.045 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A 105 "   -0.039 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A 105 "    0.119 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.33: 455
        2.33 -     2.90: 5241
        2.90 -     3.46: 5538
        3.46 -     4.03: 7334
        4.03 -     4.60: 10520
  Nonbonded interactions: 29088
  Sorted by model distance:
  nonbonded model="  12" pdb=" HZ1 LYS A  10 "
            model="  12" pdb=" OD1 ASP A  23 "
     model   vdw
     1.759 1.850
  nonbonded model="  12" pdb=" HB3 TYR A  91 "
            model="  12" pdb="HD21 LEU A  99 "
     model   vdw
     1.770 2.440
  nonbonded model="  12" pdb="HG22 ILE A  71 "
            model="  12" pdb=" HB  ILE A  77 "
     model   vdw
     1.774 2.440
  nonbonded model="  12" pdb=" OD2 ASP A  36 "
            model="  12" pdb=" HZ1 LYS A  40 "
     model   vdw
     1.779 1.850
  nonbonded model="  12" pdb=" OD1 ASP A  44 "
            model="  12" pdb=" HG  SER A  46 "
     model   vdw
     1.786 1.850
  ... (remaining 29083 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 92
        1.23 -     1.43: 382
        1.43 -     1.63: 657
        1.63 -     1.82: 5
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CA  ASP A  88 "
       model="   0" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.641 -0.116 2.10e-02 2.27e+03 3.04e+01
  bond model="   0" pdb=" N   LYS A  79 "
       model="   0" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.560 -0.102 1.90e-02 2.77e+03 2.89e+01
  bond model="   0" pdb=" C   ASP A  88 "
       model="   0" pdb=" N   TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.329  1.395 -0.066 1.40e-02 5.10e+03 2.25e+01
  bond model="   0" pdb=" N   TYR A  89 "
       model="   0" pdb=" CA  TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.525 -0.067 1.90e-02 2.77e+03 1.25e+01
  bond model="   0" pdb=" CA  GLY A  87 "
       model="   0" pdb=" C   GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.516  1.568 -0.052 1.80e-02 3.09e+03 8.44e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       91.49 -   101.23: 20
      101.23 -   110.97: 2294
      110.97 -   120.71: 1239
      120.71 -   130.45: 520
      130.45 -   140.19: 6
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   ILE A  78 "
        model="   0" pdb=" N   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  140.19  -18.49 1.80e+00 3.09e-01 1.06e+02
  angle model="   0" pdb=" CA  ILE A  51 "
        model="   0" pdb=" C   ILE A  51 "
        model="   0" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  128.28  -11.38 1.50e+00 4.44e-01 5.75e+01
  angle model="   0" pdb=" N   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
        model="   0" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.50  122.70  -12.20 1.70e+00 3.46e-01 5.15e+01
  angle model="   0" pdb=" C   SER A  97 "
        model="   0" pdb=" N   SER A  98 "
        model="   0" pdb=" CA  SER A  98 "
      ideal   model   delta    sigma   weight residual
     121.70  134.51  -12.81 1.80e+00 3.09e-01 5.06e+01
  angle model="   0" pdb=" N   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
        model="   0" pdb=" C   LYS A  79 "
      ideal   model   delta    sigma   weight residual
     111.00   91.52   19.48 2.80e+00 1.28e-01 4.84e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.28: 962
       25.28 -    50.56: 47
       50.56 -    75.84: 8
       75.84 -   101.11: 3
      101.11 -   126.39: 1
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -53.61 -126.39     0      5.00e+00 4.00e-02 6.39e+02
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   94.33   85.67     0      5.00e+00 4.00e-02 2.94e+02
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   95.22   84.78     0      5.00e+00 4.00e-02 2.88e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.127: 169
       1.127 -    2.253: 0
       2.253 -    3.379: 1
       3.379 -    4.505: 1
       4.505 -    5.632: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CB  ILE A  78 "
            model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" CG1 ILE A  78 "
            model="   0" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.99    5.63 2.00e-01 2.50e+01 7.93e+02
  chirality model="   0" pdb=" CA  LYS A  79 "
            model="   0" pdb=" N   LYS A  79 "
            model="   0" pdb=" C   LYS A  79 "
            model="   0" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.79    5.30 2.00e-01 2.50e+01 7.01e+02
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.52    5.03 2.00e-01 2.50e+01 6.33e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  GLY A  94 "    0.046 2.00e-02 2.50e+03   9.17e-02 8.40e+01
        model="   0" pdb=" C   GLY A  94 "   -0.159 2.00e-02 2.50e+03
        model="   0" pdb=" O   GLY A  94 "    0.059 2.00e-02 2.50e+03
        model="   0" pdb=" N   ASP A  95 "    0.054 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.110 2.00e-02 2.50e+03   4.88e-02 7.14e+01
        model="   0" pdb=" CG  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.101 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.029 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.006 2.00e-02 2.50e+03   4.27e-02 5.47e+01
        model="   0" pdb=" CG  TYR A  91 "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.099 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.075 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 91
        2.11 -     2.73: 3701
        2.73 -     3.35: 6513
        3.35 -     3.98: 7975
        3.98 -     4.60: 11971
  Nonbonded interactions: 30251
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A 122 "
            model="   0" pdb=" H   GLU A 123 "
     model   vdw
     1.487 2.270
  nonbonded model="   0" pdb=" H   LEU A  93 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.725 2.100
  nonbonded model="   0" pdb=" HA  TYR A  89 "
            model="   0" pdb=" H   TYR A  91 "
     model   vdw
     1.771 2.270
  nonbonded model="   0" pdb=" HG  SER A  17 "
            model="   0" pdb=" OD2 ASP A  74 "
     model   vdw
     1.845 1.850
  nonbonded model="   0" pdb=" O   ASP A   7 "
            model="   0" pdb=" HG  SER A  11 "
     model   vdw
     1.845 1.850
  ... (remaining 30246 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  87  GLY  N
   A  87  GLY  CA          1.45     1.52    -0.07  1.60e-02  2.01e+01   4.5*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.072 (Z=  4.483)
  Mean delta:    0.014 (Z=  0.733)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.27     5.33  1.00e+00  2.84e+01   5.3*sigma
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        121.70   130.78    -9.08  1.80e+00  2.55e+01   5.0*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   108.86     4.94  1.00e+00  2.44e+01   4.9*sigma
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   129.91    -8.21  1.80e+00  2.08e+01   4.6*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD2       120.80   114.13     6.67  1.50e+00  1.98e+01   4.4*sigma
   A  72  ASN  N
   A  72  ASN  CA
   A  72  ASN  C         111.00   123.25   -12.25  2.80e+00  1.92e+01   4.4*sigma
   A  72  ASN  OD1
   A  72  ASN  CG
   A  72  ASN  ND2       122.60   118.26     4.34  1.00e+00  1.88e+01   4.3*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   12.254 (Z=  5.333)
  Mean delta:    2.146 (Z=  1.165)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   -70.78  -109.22  5.00e+00  4.77e+02  21.8*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   151.57    28.43  5.00e+00  3.23e+01   5.7*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00  -153.52   -26.48  5.00e+00  2.80e+01   5.3*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   155.05    24.95  5.00e+00  2.49e+01   5.0*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -158.97   -21.03  5.00e+00  1.77e+01   4.2*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   159.63    20.37  5.00e+00  1.66e+01   4.1*sigma
   A 101  LYS  CA
   A 101  LYS  C
   A 102  PRO  N
   A 102  PRO  CA        180.00  -159.79   -20.21  5.00e+00  1.63e+01   4.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00  -159.91   -20.09  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.051
  Max. delta:  109.225
  Mean delta:   16.033

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.608
  Mean delta:    0.113

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.192       0.230      735.73  11.5*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.078       0.133      120.25   6.7*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.068       0.131       92.95   6.5*sigma
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.071       0.119      101.10   6.0*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  ND1
   A 138  HIS  CD2
   A 138  HIS  CE1
   A 138  HIS  NE2           0.088       0.118      115.96   5.9*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.052       0.103       54.79   5.2*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.042       0.082       34.66   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.192
  Mean delta:    0.023

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  72  ASN  HA , Angle N-CA-HA, observed: 96.507, delta from target: 13.493

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.072   2242  Z= 0.522
    Angle     :  1.926  13.493   4079  Z= 0.855
    Chirality :  0.113   0.608    176
    Planarity :  0.018   0.198    327
    Dihedral  : 13.901 109.225    769
    Min Nonbonded Distance : 1.632
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  5.84 %
      Favored  : 90.51 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.03 %
      Favored  : 93.55 %
    Cbeta Deviations :  1.52 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.54 (0.63), residues: 137
    helix: -1.57 (0.45), residues: 70
    sheet:  None (None), residues: 0
    loop : -1.73 (0.80), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.007   HIS A 137 
   PHE   0.068   0.012   PHE A  67 
   TYR   0.501   0.053   TYR A  89 
   ARG   0.039   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.007   HIS A 137 
   PHE   0.047   0.011   PHE A  67 
   TYR   0.378   0.060   TYR A  89 
   ARG   0.011   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 128}
  Ramachandran outliers =   3.65 %
                favored =  90.51 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     2
  Clashscore            =   7.66
  RMS(bonds)            =   0.0100
  RMS(angles)           =   1.93
  MolProbity score      =   2.25

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH1 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.323  1.283  0.040 1.40e-02 5.10e+03 8.12e+00
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.81e+00
  bond model="  10" pdb=" CD2 HIS A 136 "
       model="  10" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.51e+00
  bond model="  10" pdb=" CZ  ARG A 127 "
       model="  10" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.48e+00
  bond model="  10" pdb=" CD2 HIS A 137 "
       model="  10" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.06e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.52 -   105.50: 92
      105.50 -   111.47: 2387
      111.47 -   117.45: 573
      117.45 -   123.42: 861
      123.42 -   129.40: 166
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  10" pdb=" OE1 GLN A  66 "
        model="  10" pdb=" CD  GLN A  66 "
        model="  10" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.43    4.17 1.00e+00 1.00e+00 1.74e+01
  angle model="  10" pdb=" CG1 VAL A  41 "
        model="  10" pdb=" CB  VAL A  41 "
        model="  10" pdb=" CG2 VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.80  101.78    9.02 2.20e+00 2.07e-01 1.68e+01
  angle model="  10" pdb=" OE1 GLN A  28 "
        model="  10" pdb=" CD  GLN A  28 "
        model="  10" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.54    4.06 1.00e+00 1.00e+00 1.65e+01
  angle model="  10" pdb=" N   ASP A  88 "
        model="  10" pdb=" CA  ASP A  88 "
        model="  10" pdb=" CB  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     110.50  104.03    6.47 1.70e+00 3.46e-01 1.45e+01
  angle model="  10" pdb=" C   THR A  82 "
        model="  10" pdb=" N   THR A  83 "
        model="  10" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  127.91   -6.21 1.80e+00 3.09e-01 1.19e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 920
       17.43 -    34.85: 69
       34.85 -    52.28: 26
       52.28 -    69.70: 14
       69.70 -    87.13: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  10" pdb=" CA  MET A   1 "
           model="  10" pdb=" C   MET A   1 "
           model="  10" pdb=" N   LEU A   2 "
           model="  10" pdb=" CA  LEU A   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -141.67  -38.33     0      5.00e+00 4.00e-02 5.88e+01
  dihedral model="  10" pdb=" CA  PRO A 114 "
           model="  10" pdb=" C   PRO A 114 "
           model="  10" pdb=" N   ALA A 115 "
           model="  10" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.45   25.55     0      5.00e+00 4.00e-02 2.61e+01
  dihedral model="  10" pdb=" CA  ALA A 115 "
           model="  10" pdb=" C   ALA A 115 "
           model="  10" pdb=" N   ASP A 116 "
           model="  10" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.53  -18.47     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 74
       0.049 -    0.098: 51
       0.098 -    0.147: 29
       0.147 -    0.196: 18
       0.196 -    0.245: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CA  VAL A 112 "
            model="  10" pdb=" N   VAL A 112 "
            model="  10" pdb=" C   VAL A 112 "
            model="  10" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.24 2.00e-01 2.50e+01 1.50e+00
  chirality model="  10" pdb=" CA  PHE A  45 "
            model="  10" pdb=" N   PHE A  45 "
            model="  10" pdb=" C   PHE A  45 "
            model="  10" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality model="  10" pdb=" CB  VAL A  41 "
            model="  10" pdb=" CA  VAL A  41 "
            model="  10" pdb=" CG1 VAL A  41 "
            model="  10" pdb=" CG2 VAL A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.84    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A 111 "    0.144 2.00e-02 2.50e+03   5.40e-02 8.75e+01
        model="  10" pdb=" CG  TYR A 111 "   -0.033 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A 111 "   -0.036 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A 111 "   -0.034 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A 111 "    0.067 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A 111 "   -0.058 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A 111 "   -0.052 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  12 "   -0.090 2.00e-02 2.50e+03   4.14e-02 5.13e+01
        model="  10" pdb=" CG  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  12 "   -0.089 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  12 "    0.035 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  12 "    0.028 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  12 "    0.022 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  12 "    0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  HIS A  43 "    0.056 2.00e-02 2.50e+03   4.74e-02 4.49e+01
        model="  10" pdb=" CG  HIS A  43 "   -0.029 2.00e-02 2.50e+03
        model="  10" pdb=" ND1 HIS A  43 "   -0.082 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 HIS A  43 "   -0.008 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 HIS A  43 "    0.002 2.00e-02 2.50e+03
        model="  10" pdb=" NE2 HIS A  43 "   -0.033 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 HIS A  43 "    0.018 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 HIS A  43 "    0.076 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 271
        2.27 -     2.85: 4848
        2.85 -     3.44: 5420
        3.44 -     4.02: 6749
        4.02 -     4.60: 10100
  Nonbonded interactions: 27388
  Sorted by model distance:
  nonbonded model="  10" pdb=" H   LEU A   3 "
            model="  10" pdb=" HG  LEU A   3 "
     model   vdw
     1.690 2.270
  nonbonded model="  10" pdb="HD22 LEU A   3 "
            model="  10" pdb=" HG  LEU A  53 "
     model   vdw
     1.784 2.440
  nonbonded model="  10" pdb=" OE2 GLU A  16 "
            model="  10" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.815 1.850
  nonbonded model="  10" pdb="HH12 ARG A  21 "
            model="  10" pdb=" HB2 ASN A  72 "
     model   vdw
     1.837 2.270
  nonbonded model="  10" pdb=" HG1 THR A   5 "
            model="  10" pdb=" OE1 GLU A   8 "
     model   vdw
     1.839 1.850
  ... (remaining 27383 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.12 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.04, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (35.217, 50.458, 70.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ILE A  77 "
        model="   2" pdb=" CB  ILE A  78 "
        model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CB  TYR A  89 "
        model="   2" pdb=" CB  THR A  92 "
        model="   2" pdb=" CB  SER A  98 "
  Number of C-beta restraints generated:  250

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   0" pdb=" CB  ILE A  51 "
        model="   0" pdb=" CB  ILE A  78 "
        model="   0" pdb=" CB  LYS A  79 "
        model="   0" pdb=" CB  TYR A  89 "
        model="   0" pdb=" CB  SER A  97 "
        model="   0" pdb=" CB  SER A  98 "
        model="   0" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  250

  Time building geometry restraints manager: 1.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 77
        1.23 -     1.42: 395
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH1 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.323  1.280  0.043 1.40e-02 5.10e+03 9.44e+00
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.29e+00
  bond model="  10" pdb=" CD2 HIS A 139 "
       model="  10" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.43e+00
  bond model="  10" pdb=" CD2 HIS A 136 "
       model="  10" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.78e+00
  bond model="  10" pdb=" CD2 HIS A 138 "
       model="  10" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.67e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.49 -   105.53: 90
      105.53 -   111.58: 2416
      111.58 -   117.62: 560
      117.62 -   123.67: 874
      123.67 -   129.71: 139
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  10" pdb=" C   LEU A   2 "
        model="  10" pdb=" N   LEU A   3 "
        model="  10" pdb=" CA  LEU A   3 "
      ideal   model   delta    sigma   weight residual
     121.70  129.71   -8.01 1.80e+00 3.09e-01 1.98e+01
  angle model="  10" pdb=" OE1 GLN A  28 "
        model="  10" pdb=" CD  GLN A  28 "
        model="  10" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.30    4.30 1.00e+00 1.00e+00 1.85e+01
  angle model="  10" pdb=" OE1 GLN A  66 "
        model="  10" pdb=" CD  GLN A  66 "
        model="  10" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.75    3.85 1.00e+00 1.00e+00 1.48e+01
  angle model="  10" pdb=" OE1 GLN A 100 "
        model="  10" pdb=" CD  GLN A 100 "
        model="  10" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.10    3.50 1.00e+00 1.00e+00 1.23e+01
  angle model="  10" pdb=" N   LEU A   3 "
        model="  10" pdb=" CA  LEU A   3 "
        model="  10" pdb=" CB  LEU A   3 "
      ideal   model   delta    sigma   weight residual
     110.50  104.65    5.85 1.70e+00 3.46e-01 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 919
       17.47 -    34.93: 71
       34.93 -    52.39: 25
       52.39 -    69.86: 12
       69.86 -    87.32: 6
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  10" pdb=" CA  ALA A 115 "
           model="  10" pdb=" C   ALA A 115 "
           model="  10" pdb=" N   ASP A 116 "
           model="  10" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.05  -23.95     0      5.00e+00 4.00e-02 2.29e+01
  dihedral model="  10" pdb=" CA  GLY A  73 "
           model="  10" pdb=" C   GLY A  73 "
           model="  10" pdb=" N   ASP A  74 "
           model="  10" pdb=" CA  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.60  -18.40     0      5.00e+00 4.00e-02 1.35e+01
  dihedral model="  10" pdb=" C   ILE A  78 "
           model="  10" pdb=" N   ILE A  78 "
           model="  10" pdb=" CA  ILE A  78 "
           model="  10" pdb=" CB  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.58    8.58     0      2.50e+00 1.60e-01 1.18e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 67
       0.046 -    0.092: 48
       0.092 -    0.138: 35
       0.138 -    0.184: 22
       0.184 -    0.230: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CG  LEU A  39 "
            model="  10" pdb=" CB  LEU A  39 "
            model="  10" pdb=" CD1 LEU A  39 "
            model="  10" pdb=" CD2 LEU A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality model="  10" pdb=" CA  VAL A 112 "
            model="  10" pdb=" N   VAL A 112 "
            model="  10" pdb=" C   VAL A 112 "
            model="  10" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.55e-01
  chirality model="  10" pdb=" CA  THR A  82 "
            model="  10" pdb=" N   THR A  82 "
            model="  10" pdb=" C   THR A  82 "
            model="  10" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.96e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  PHE A  45 "    0.049 2.00e-02 2.50e+03   5.92e-02 1.05e+02
        model="  10" pdb=" CG  PHE A  45 "   -0.014 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 PHE A  45 "   -0.043 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 PHE A  45 "    0.019 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 PHE A  45 "    0.028 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 PHE A  45 "   -0.034 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  PHE A  45 "    0.011 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 PHE A  45 "   -0.108 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 PHE A  45 "    0.075 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 PHE A  45 "    0.085 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 PHE A  45 "   -0.099 2.00e-02 2.50e+03
        model="  10" pdb=" HZ  PHE A  45 "    0.031 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  68 "    0.073 2.00e-02 2.50e+03   5.04e-02 7.63e+01
        model="  10" pdb=" CG  TYR A  68 "   -0.006 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  68 "   -0.007 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  68 "   -0.015 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  68 "   -0.033 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  68 "   -0.024 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  68 "   -0.013 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  68 "    0.131 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  68 "    0.010 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  68 "   -0.015 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  68 "   -0.064 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  68 "   -0.037 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  12 "   -0.100 2.00e-02 2.50e+03   4.61e-02 6.37e+01
        model="  10" pdb=" CG  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  12 "   -0.098 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  12 "    0.046 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  12 "    0.027 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  12 "    0.035 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 222
        2.23 -     2.83: 4534
        2.83 -     3.42: 5889
        3.42 -     4.01: 7056
        4.01 -     4.60: 10486
  Nonbonded interactions: 28187
  Sorted by model distance:
  nonbonded model="  10" pdb="HD13 LEU A   3 "
            model="  10" pdb="HD12 LEU A  53 "
     model   vdw
     1.643 2.440
  nonbonded model="  10" pdb="HH22 ARG A  21 "
            model="  10" pdb=" HB3 ASN A  72 "
     model   vdw
     1.666 2.270
  nonbonded model="  10" pdb=" H   LEU A   3 "
            model="  10" pdb=" HG  LEU A   3 "
     model   vdw
     1.685 2.270
  nonbonded model="  10" pdb="HG23 ILE A  78 "
            model="  10" pdb=" H   LYS A  79 "
     model   vdw
     1.710 2.270
  nonbonded model="  10" pdb=" OE2 GLU A  24 "
            model="  10" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.757 1.850
  ... (remaining 28182 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 60
        1.23 -     1.43: 415
        1.43 -     1.62: 657
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" N   SER A  98 "
       model="   0" pdb=" CA  SER A  98 "
    ideal  model  delta    sigma   weight residual
    1.458  1.380  0.078 1.90e-02 2.77e+03 1.67e+01
  bond model="   0" pdb=" CA  LYS A  79 "
       model="   0" pdb=" CB  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.530  1.602 -0.072 2.00e-02 2.50e+03 1.28e+01
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.76e+00
  bond model="   0" pdb=" CA  ASP A  88 "
       model="   0" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.583 -0.058 2.10e-02 2.27e+03 7.61e+00
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.48e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       82.31 -    93.39: 4
       93.39 -   104.48: 69
      104.48 -   115.56: 2903
      115.56 -   126.65: 1068
      126.65 -   137.73: 35
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   TYR A  89 "
        model="   0" pdb=" CA  TYR A  89 "
        model="   0" pdb=" CB  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.10  134.46  -24.36 1.90e+00 2.77e-01 1.64e+02
  angle model="   0" pdb=" C   ILE A  78 "
        model="   0" pdb=" N   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  137.73  -16.03 1.80e+00 3.09e-01 7.94e+01
  angle model="   0" pdb=" CB  TYR A  89 "
        model="   0" pdb=" CA  TYR A  89 "
        model="   0" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   82.31   26.69 3.00e+00 1.11e-01 7.92e+01
  angle model="   0" pdb=" C   SER A  90 "
        model="   0" pdb=" CA  SER A  90 "
        model="   0" pdb=" CB  SER A  90 "
      ideal   model   delta    sigma   weight residual
     110.10  126.55  -16.45 1.90e+00 2.77e-01 7.49e+01
  angle model="   0" pdb=" C   LEU A  93 "
        model="   0" pdb=" CA  LEU A  93 "
        model="   0" pdb=" CB  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.10   94.57   15.53 1.90e+00 2.77e-01 6.68e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.14: 969
       25.14 -    50.29: 37
       50.29 -    75.43: 9
       75.43 -   100.58: 2
      100.58 -   125.72: 2
  Dihedral angle restraints: 1019
    sinusoidal: 562
      harmonic: 457
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -54.28 -125.72     0      5.00e+00 4.00e-02 6.32e+02
  dihedral model="   0" pdb=" CA  TYR A  91 "
           model="   0" pdb=" C   TYR A  91 "
           model="   0" pdb=" N   THR A  92 "
           model="   0" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -64.87 -115.13     0      5.00e+00 4.00e-02 5.30e+02
  dihedral model="   0" pdb=" CA  ILE A  78 "
           model="   0" pdb=" C   ILE A  78 "
           model="   0" pdb=" N   LYS A  79 "
           model="   0" pdb=" CA  LYS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -91.66  -88.34     0      5.00e+00 4.00e-02 3.12e+02
  ... (remaining 1016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.003 -    1.184: 168
       1.184 -    2.365: 0
       2.365 -    3.545: 1
       3.545 -    4.726: 1
       4.726 -    5.907: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  79 "
            model="   0" pdb=" N   LYS A  79 "
            model="   0" pdb=" C   LYS A  79 "
            model="   0" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.40    5.91 2.00e-01 2.50e+01 8.72e+02
  chirality model="   0" pdb=" CB  ILE A  78 "
            model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" CG1 ILE A  78 "
            model="   0" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.62    5.26 2.00e-01 2.50e+01 6.92e+02
  chirality model="   0" pdb=" CA  HIS A 139 "
            model="   0" pdb=" N   HIS A 139 "
            model="   0" pdb=" C   HIS A 139 "
            model="   0" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.49    5.00 2.00e-01 2.50e+01 6.25e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.250 2.00e-02 2.50e+03   1.07e-01 3.40e+02
        model="   0" pdb=" CG  TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.050 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.197 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.090 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.106 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.049 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.244 2.00e-02 2.50e+03   9.52e-02 2.72e+02
        model="   0" pdb=" CG  TYR A  89 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.050 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.064 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.131 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.081 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.122 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.105 2.00e-02 2.50e+03   4.75e-02 6.76e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.095 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.047 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 92
        2.09 -     2.72: 3591
        2.72 -     3.34: 6455
        3.34 -     3.97: 7947
        3.97 -     4.60: 12018
  Nonbonded interactions: 30103
  Sorted by model distance:
  nonbonded model="   0" pdb=" H   SER A  90 "
            model="   0" pdb=" HA  TYR A  91 "
     model   vdw
     1.462 2.270
  nonbonded model="   0" pdb=" HA  ILE A  77 "
            model="   0" pdb=" HB2 LYS A  79 "
     model   vdw
     1.486 2.440
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" H   THR A  92 "
     model   vdw
     1.729 2.270
  nonbonded model="   0" pdb=" H   LEU A  93 "
            model="   0" pdb=" HA  SER A  98 "
     model   vdw
     1.753 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.758 1.850
  ... (remaining 30098 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 60
        1.23 -     1.43: 414
        1.43 -     1.62: 654
        1.62 -     1.82: 8
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" CA  SER A  98 "
       model="   2" pdb=" C   SER A  98 "
    ideal  model  delta    sigma   weight residual
    1.525  1.697 -0.172 2.10e-02 2.27e+03 6.69e+01
  bond model="   2" pdb=" N   LEU A  99 "
       model="   2" pdb=" CA  LEU A  99 "
    ideal  model  delta    sigma   weight residual
    1.458  1.607 -0.149 1.90e-02 2.77e+03 6.17e+01
  bond model="   2" pdb=" CA  TYR A  91 "
       model="   2" pdb=" C   TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.525  1.676 -0.151 2.10e-02 2.27e+03 5.18e+01
  bond model="   2" pdb=" C   SER A  98 "
       model="   2" pdb=" N   LEU A  99 "
    ideal  model  delta    sigma   weight residual
    1.329  1.414 -0.085 1.40e-02 5.10e+03 3.65e+01
  bond model="   2" pdb=" CA  LEU A  99 "
       model="   2" pdb=" C   LEU A  99 "
    ideal  model  delta    sigma   weight residual
    1.525  1.637 -0.112 2.10e-02 2.27e+03 2.84e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       74.58 -    88.33: 5
       88.33 -   102.07: 31
      102.07 -   115.82: 2935
      115.82 -   129.56: 1088
      129.56 -   143.31: 20
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" C   SER A  98 "
        model="   2" pdb=" N   LEU A  99 "
        model="   2" pdb=" CA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     121.70  143.31  -21.61 1.80e+00 3.09e-01 1.44e+02
  angle model="   2" pdb=" C   SER A  98 "
        model="   2" pdb=" CA  SER A  98 "
        model="   2" pdb=" HA  SER A  98 "
      ideal   model   delta    sigma   weight residual
     109.00   74.58   34.42 3.00e+00 1.11e-01 1.32e+02
  angle model="   2" pdb=" CB  SER A  98 "
        model="   2" pdb=" CA  SER A  98 "
        model="   2" pdb=" HA  SER A  98 "
      ideal   model   delta    sigma   weight residual
     109.00  140.00  -31.00 3.00e+00 1.11e-01 1.07e+02
  angle model="   2" pdb=" N   SER A  98 "
        model="   2" pdb=" CA  SER A  98 "
        model="   2" pdb=" C   SER A  98 "
      ideal   model   delta    sigma   weight residual
     111.00  138.58  -27.58 2.80e+00 1.28e-01 9.70e+01
  angle model="   2" pdb=" C   TYR A  91 "
        model="   2" pdb=" CA  TYR A  91 "
        model="   2" pdb=" CB  TYR A  91 "
      ideal   model   delta    sigma   weight residual
     110.10  126.49  -16.39 1.90e+00 2.77e-01 7.44e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.63: 895
       16.63 -    33.26: 75
       33.26 -    49.88: 29
       49.88 -    66.51: 13
       66.51 -    83.14: 7
  Dihedral angle restraints: 1019
    sinusoidal: 562
      harmonic: 457
  Sorted by residual:
  dihedral model="   2" pdb=" CA  LEU A  93 "
           model="   2" pdb=" C   LEU A  93 "
           model="   2" pdb=" N   GLY A  94 "
           model="   2" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  100.74   79.26     0      5.00e+00 4.00e-02 2.51e+02
  dihedral model="   2" pdb=" CA  SER A  90 "
           model="   2" pdb=" C   SER A  90 "
           model="   2" pdb=" N   TYR A  91 "
           model="   2" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -101.64  -78.36     0      5.00e+00 4.00e-02 2.46e+02
  dihedral model="   2" pdb=" CA  THR A  92 "
           model="   2" pdb=" C   THR A  92 "
           model="   2" pdb=" N   LEU A  93 "
           model="   2" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -102.11  -77.89     0      5.00e+00 4.00e-02 2.43e+02
  ... (remaining 1016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.096: 166
       1.096 -    2.192: 1
       2.192 -    3.287: 0
       3.287 -    4.383: 2
       4.383 -    5.479: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CA  LYS A  79 "
            model="   2" pdb=" N   LYS A  79 "
            model="   2" pdb=" C   LYS A  79 "
            model="   2" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.97    5.48 2.00e-01 2.50e+01 7.50e+02
  chirality model="   2" pdb=" CA  THR A  92 "
            model="   2" pdb=" N   THR A  92 "
            model="   2" pdb=" C   THR A  92 "
            model="   2" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -2.76    5.29 2.00e-01 2.50e+01 6.99e+02
  chirality model="   2" pdb=" CB  ILE A  78 "
            model="   2" pdb=" CA  ILE A  78 "
            model="   2" pdb=" CG1 ILE A  78 "
            model="   2" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.53    5.17 2.00e-01 2.50e+01 6.69e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  89 "    0.199 2.00e-02 2.50e+03   8.54e-02 2.19e+02
        model="   2" pdb=" CG  TYR A  89 "    0.014 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  89 "   -0.043 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  89 "   -0.040 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  89 "   -0.022 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  89 "   -0.018 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  89 "    0.035 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  89 "    0.147 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  89 "   -0.094 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  89 "   -0.090 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  89 "   -0.047 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  89 "   -0.039 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  12 "    0.090 2.00e-02 2.50e+03   4.11e-02 5.08e+01
        model="   2" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  12 "   -0.022 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  12 "    0.086 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  12 "   -0.042 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  12 "   -0.038 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  91 "    0.044 2.00e-02 2.50e+03   4.11e-02 5.08e+01
        model="   2" pdb=" CG  TYR A  91 "   -0.105 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  91 "   -0.025 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  91 "   -0.009 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  91 "   -0.025 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  91 "    0.055 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  91 "    0.054 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  91 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     1.95: 36
        1.95 -     2.61: 2523
        2.61 -     3.28: 7089
        3.28 -     3.94: 8604
        3.94 -     4.60: 12843
  Nonbonded interactions: 31095
  Sorted by model distance:
  nonbonded model="   2" pdb="HG22 THR A  92 "
            model="   2" pdb=" HA  LEU A  93 "
     model   vdw
     1.291 2.440
  nonbonded model="   2" pdb=" H   ILE A  78 "
            model="   2" pdb="HG21 THR A  92 "
     model   vdw
     1.451 2.270
  nonbonded model="   2" pdb=" HA  TYR A  91 "
            model="   2" pdb=" H   GLN A 100 "
     model   vdw
     1.519 2.270
  nonbonded model="   2" pdb=" HB3 TYR A  91 "
            model="   2" pdb=" HA  LEU A  99 "
     model   vdw
     1.596 2.440
  nonbonded model="   2" pdb="HD23 LEU A  93 "
            model="   2" pdb=" H   GLY A  94 "
     model   vdw
     1.654 2.270
  ... (remaining 31090 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.76 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.44e+00
  bond model="   9" pdb=" CZ  ARG A 129 "
       model="   9" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 7.06e-02
  bond model="   9" pdb=" CZ  ARG A  21 "
       model="   9" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.60e-02
  bond model="   9" pdb=" CZ  ARG A 127 "
       model="   9" pdb=" NH1 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 5.39e-02
  bond model="   9" pdb=" CD  ARG A  21 "
       model="   9" pdb=" NE  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.458  1.461 -0.003 1.40e-02 5.10e+03 5.27e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.86 -   106.86: 62
      106.86 -   112.86: 2723
      112.86 -   118.87: 426
      118.87 -   124.87: 824
      124.87 -   130.87: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A  22 "
        model="   9" pdb=" CA  PRO A  22 "
        model="   9" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   9" pdb=" CB  PRO A  52 "
        model="   9" pdb=" CA  PRO A  52 "
        model="   9" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   9" pdb=" CB  PRO A   6 "
        model="   9" pdb=" CA  PRO A   6 "
        model="   9" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   9" pdb=" CB  PRO A 117 "
        model="   9" pdb=" CA  PRO A 117 "
        model="   9" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A 102 "
        model="   9" pdb=" CA  PRO A 102 "
        model="   9" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 880
       16.92 -    33.84: 76
       33.84 -    50.76: 42
       50.76 -    67.68: 31
       67.68 -    84.60: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CA  ASP A  88 "
           model="   9" pdb=" CB  ASP A  88 "
           model="   9" pdb=" CG  ASP A  88 "
           model="   9" pdb=" OD1 ASP A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.71   56.71     1      2.00e+01 2.50e-03 1.08e+01
  dihedral model="   9" pdb=" CA  ASP A 118 "
           model="   9" pdb=" CB  ASP A 118 "
           model="   9" pdb=" CG  ASP A 118 "
           model="   9" pdb=" OD1 ASP A 118 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.26   55.26     1      2.00e+01 2.50e-03 1.03e+01
  dihedral model="   9" pdb=" CB  GLU A 120 "
           model="   9" pdb=" CG  GLU A 120 "
           model="   9" pdb=" CD  GLU A 120 "
           model="   9" pdb=" OE1 GLU A 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.60   84.60     1      3.00e+01 1.11e-03 9.66e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.019: 98
       0.019 -    0.038: 53
       0.038 -    0.057: 6
       0.057 -    0.076: 0
       0.076 -    0.094: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A   4 "
            model="   9" pdb=" N   ILE A   4 "
            model="   9" pdb=" C   ILE A   4 "
            model="   9" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.23e-01
  chirality model="   9" pdb=" CA  ILE A  38 "
            model="   9" pdb=" N   ILE A  38 "
            model="   9" pdb=" C   ILE A  38 "
            model="   9" pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.20e-01
  chirality model="   9" pdb=" CA  ILE A 122 "
            model="   9" pdb=" N   ILE A 122 "
            model="   9" pdb=" C   ILE A 122 "
            model="   9" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.14e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  12 "    0.000 2.00e-02 2.50e+03   1.09e-03 3.57e-02
        model="   9" pdb=" CG  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  12 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A 105 "    0.001 2.00e-02 2.50e+03   1.05e-03 3.31e-02
        model="   9" pdb=" CG  TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A 105 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A 105 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A  81 "    0.000 2.00e-02 2.50e+03   1.05e-03 3.28e-02
        model="   9" pdb=" CG  TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A  81 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A  81 "   -0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A  81 "    0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 136
        2.14 -     2.76: 4282
        2.76 -     3.37: 5955
        3.37 -     3.99: 7158
        3.99 -     4.60: 10954
  Nonbonded interactions: 28485
  Sorted by model distance:
  nonbonded model="   9" pdb="HD23 LEU A   9 "
            model="   9" pdb="HD22 LEU A  26 "
     model   vdw
     1.527 2.440
  nonbonded model="   9" pdb="HD13 LEU A   3 "
            model="   9" pdb="HG21 ILE A  51 "
     model   vdw
     1.588 2.440
  nonbonded model="   9" pdb="HD11 LEU A  93 "
            model="   9" pdb="HD13 LEU A  99 "
     model   vdw
     1.696 2.440
  nonbonded model="   9" pdb=" HA  LYS A  27 "
            model="   9" pdb="HD12 ILE A  30 "
     model   vdw
     1.756 2.440
  nonbonded model="   9" pdb="HG22 ILE A  78 "
            model="   9" pdb=" H   GLY A  80 "
     model   vdw
     1.759 2.270
  ... (remaining 28480 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 126  VAL  CA
   A 126  VAL  C           1.52     1.40     0.12  2.10e-02  3.37e+01   5.8*sigma
   A 125  LYS  CA
   A 125  LYS  C           1.52     1.42     0.11  2.10e-02  2.72e+01   5.2*sigma
   A 125  LYS  N
   A 125  LYS  CA          1.46     1.55    -0.09  1.90e-02  2.11e+01   4.6*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.52    -0.07  1.60e-02  1.89e+01   4.3*sigma
   A 124  ALA  C
   A 125  LYS  N           1.33     1.39    -0.06  1.40e-02  1.88e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.122 (Z=  5.808)
  Mean delta:    0.017 (Z=  0.870)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   142.39   -20.69  1.80e+00  1.32e+02  11.5*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   104.34    17.36  1.80e+00  9.30e+01   9.6*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   126.49   -15.99  1.70e+00  8.84e+01   9.4*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   126.71   -15.21  1.70e+00  8.00e+01   8.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   101.24    14.96  2.00e+00  5.60e+01   7.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.78   -10.88  1.50e+00  5.26e+01   7.3*sigma
   A 126  VAL  O
   A 126  VAL  C
   A 127  ARG  N         123.00   133.60   -10.60  1.60e+00  4.39e+01   6.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   103.19    13.01  2.00e+00  4.23e+01   6.5*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   110.11    11.59  1.80e+00  4.14e+01   6.4*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   103.51    12.69  2.00e+00  4.02e+01   6.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.60   -10.90  1.80e+00  3.67e+01   6.1*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   121.49   -11.39  1.90e+00  3.59e+01   6.0*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   101.45    10.05  1.70e+00  3.49e+01   5.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.48    -5.88  1.00e+00  3.46e+01   5.9*sigma
   A 125  LYS  O
   A 125  LYS  C
   A 126  VAL  N         123.00   132.16    -9.16  1.60e+00  3.28e+01   5.7*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   126.70   -15.70  2.80e+00  3.14e+01   5.6*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   131.74   -10.04  1.80e+00  3.11e+01   5.6*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   121.71   -10.31  1.90e+00  2.95e+01   5.4*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    96.60    14.40  2.80e+00  2.64e+01   5.1*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   119.01    -8.51  1.70e+00  2.51e+01   5.0*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   118.81    -8.41  1.70e+00  2.45e+01   4.9*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   106.38     9.82  2.00e+00  2.41e+01   4.9*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   121.40    -9.80  2.00e+00  2.40e+01   4.9*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   118.54    -8.14  1.70e+00  2.29e+01   4.8*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   130.30    -8.60  1.80e+00  2.28e+01   4.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.11    -9.51  2.00e+00  2.26e+01   4.8*sigma
   A  67  PHE  C
   A  67  PHE  CA
   A  67  PHE  CB        110.10   119.09    -8.99  1.90e+00  2.24e+01   4.7*sigma
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        121.70   130.18    -8.48  1.80e+00  2.22e+01   4.7*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00    97.96    13.04  2.80e+00  2.17e+01   4.7*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   118.34    -7.84  1.70e+00  2.13e+01   4.6*sigma
   A 125  LYS  C
   A 125  LYS  CA
   A 125  LYS  CB        110.10   118.77    -8.67  1.90e+00  2.08e+01   4.6*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   107.08     9.12  2.00e+00  2.08e+01   4.6*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   129.85    -8.15  1.80e+00  2.05e+01   4.5*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.09    -4.49  1.00e+00  2.02e+01   4.5*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG2       110.50   118.12    -7.62  1.70e+00  2.01e+01   4.5*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   129.58    -7.88  1.80e+00  1.92e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.53     5.67  1.30e+00  1.90e+01   4.4*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   118.38    -8.28  1.90e+00  1.90e+01   4.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   107.59     8.61  2.00e+00  1.85e+01   4.3*sigma
   A  97  SER  O
   A  97  SER  C
   A  98  SER  N         123.00   129.84    -6.84  1.60e+00  1.83e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.35     4.25  1.00e+00  1.81e+01   4.2*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   129.34    -7.64  1.80e+00  1.80e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.75e+01   4.2*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   107.88     8.32  2.00e+00  1.73e+01   4.2*sigma
   A  93  LEU  CA
   A  93  LEU  CB
   A  93  LEU  CG        116.30   130.71   -14.41  3.50e+00  1.70e+01   4.1*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   129.06    -7.36  1.80e+00  1.67e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   20.694 (Z= 11.497)
  Mean delta:    2.873 (Z=  1.547)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00    78.89   101.11  5.00e+00  4.09e+02  20.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00    83.85    96.15  5.00e+00  3.70e+02  19.2*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   -88.41   -91.59  5.00e+00  3.36e+02  18.3*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00    89.48    90.52  5.00e+00  3.28e+02  18.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   105.83    74.17  5.00e+00  2.20e+02  14.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   116.41    63.59  5.00e+00  1.62e+02  12.7*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   118.23    61.77  5.00e+00  1.53e+02  12.4*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   121.22    58.78  5.00e+00  1.38e+02  11.8*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   131.01    48.99  5.00e+00  9.60e+01   9.8*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -131.86   -48.14  5.00e+00  9.27e+01   9.6*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -131.86   -48.14  5.00e+00  9.27e+01   9.6*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00  -138.57   -41.43  5.00e+00  6.87e+01   8.3*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   138.66    41.34  5.00e+00  6.84e+01   8.3*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   140.60    39.40  5.00e+00  6.21e+01   7.9*sigma
   A 100  GLN  CA
   A 100  GLN  C
   A 101  LYS  N
   A 101  LYS  CA        180.00   142.05    37.95  5.00e+00  5.76e+01   7.6*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   142.16    37.84  5.00e+00  5.73e+01   7.6*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   147.51    32.49  5.00e+00  4.22e+01   6.5*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   150.68    29.32  5.00e+00  3.44e+01   5.9*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00  -151.26   -28.74  5.00e+00  3.30e+01   5.7*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   153.65    26.35  5.00e+00  2.78e+01   5.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   154.90    25.10  5.00e+00  2.52e+01   5.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   155.52    24.48  5.00e+00  2.40e+01   4.9*sigma
   A 102  PRO  CA
   A 102  PRO  C
   A 103  ASP  N
   A 103  ASP  CA        180.00  -155.98   -24.02  5.00e+00  2.31e+01   4.8*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   156.85    23.15  5.00e+00  2.14e+01   4.6*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   157.95    22.05  5.00e+00  1.95e+01   4.4*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -158.70   -21.30  5.00e+00  1.82e+01   4.3*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   158.83    21.17  5.00e+00  1.79e+01   4.2*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -159.80   -20.20  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.066
  Max. delta:  101.110
  Mean delta:   20.224

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.62     5.27  2.00e-01  6.94e+02  26.3*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.74     5.25  2.00e-01  6.88e+02  26.2*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.35     4.86  2.00e-01  5.91e+02  24.3*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51    -2.30     4.81  2.00e-01  5.78e+02  24.0*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.37     4.81  2.00e-01  5.77e+02  24.0*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.10     4.61  2.00e-01  5.31e+02  23.0*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -1.68     4.12  2.00e-01  4.24e+02  20.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.06     3.49  2.00e-01  3.05e+02  17.5*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     0.96     1.55  2.00e-01  6.02e+01   7.8*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51     1.45     1.06  2.00e-01  2.83e+01   5.3*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     1.45     1.06  2.00e-01  2.82e+01   5.3*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     1.67     0.84  2.00e-01  1.75e+01   4.2*sigma

  Min. delta:    0.000
  Max. delta:    5.269
  Mean delta:    1.025

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.145
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 127  ARG  HA , Angle C-CA-HA, observed: 96.701, delta from target: 12.299
   A 130  SER  HA , Angle N-CA-HA, observed: 95.308, delta from target: 14.692
   A 125  LYS  HA , Angle CB-CA-HA, observed: 94.242, delta from target: 14.758
   A  51  ILE  HA , Angle CB-CA-HA, observed: 94.124, delta from target: 14.876
   A 126  VAL  HB , Angle CA-CB-HB, observed: 93.395, delta from target: 15.605
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.127, delta from target: 15.873
   A  90  SER  HA , Angle CB-CA-HA, observed: 92.801, delta from target: 16.199
   A  90  SER  HA , Angle N-CA-HA, observed: 92.034, delta from target: 17.966
   A 127  ARG  HA , Angle CB-CA-HA, observed: 88.692, delta from target: 20.308
   A  89  TYR  HA , Angle C-CA-HA, observed: 84.995, delta from target: 24.005
   A 126  VAL  HA , Angle CB-CA-HA, observed: 80.191, delta from target: 28.809

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.122   2242  Z= 0.620
    Angle     :  2.538  28.809   4079  Z= 1.128
    Chirality :  1.025   5.269    176
    Planarity :  0.013   0.113    327
    Dihedral  : 16.425 101.110    769
    Min Nonbonded Distance : 1.436
  
  Molprobity Statistics.
    All-atom Clashscore : 13.53
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  : 11.68 %
      Favored  : 80.29 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  7.26 %
      Favored  : 85.48 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 12.98 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.58 (0.68), residues: 137
    helix: -1.64 (0.55), residues: 62
    sheet:  None (None), residues: 0
    loop : -3.15 (0.75), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A  43 
   PHE   0.126   0.019   PHE A  67 
   TYR   0.079   0.017   TYR A  50 
   ARG   0.117   0.014   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A  43 
   PHE   0.079   0.020   PHE A  67 
   TYR   0.070   0.018   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   8.03 %
                favored =  80.29 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    16
  Clashscore            =  13.53
  RMS(bonds)            =   0.0119
  RMS(angles)           =   2.54
  MolProbity score      =   3.03

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  ILE A  78 "
        model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CB  TYR A  89 "
        model="   5" pdb=" CB  ASP A 116 "
  Number of C-beta restraints generated:  254

  Time building geometry restraints manager: 0.97 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 42
        1.23 -     1.42: 432
        1.42 -     1.62: 658
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" N   GLY A  80 "
       model="   5" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.537 -0.086 1.60e-02 3.91e+03 2.87e+01
  bond model="   5" pdb=" C   ILE A  77 "
       model="   5" pdb=" N   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.329  1.270  0.059 1.40e-02 5.10e+03 1.76e+01
  bond model="   5" pdb=" CA  LYS A  79 "
       model="   5" pdb=" CB  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.530  1.597 -0.067 2.00e-02 2.50e+03 1.14e+01
  bond model="   5" pdb=" CA  THR A  92 "
       model="   5" pdb=" C   THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.525  1.464  0.061 2.10e-02 2.27e+03 8.46e+00
  bond model="   5" pdb=" N   LYS A  79 "
       model="   5" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.512 -0.054 1.90e-02 2.77e+03 8.19e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       78.90 -    90.92: 2
       90.92 -   102.94: 51
      102.94 -   114.97: 2875
      114.97 -   126.99: 1125
      126.99 -   139.01: 26
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" C   ILE A  78 "
        model="   5" pdb=" CA  ILE A  78 "
        model="   5" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   78.90   30.10 3.00e+00 1.11e-01 1.01e+02
  angle model="   5" pdb=" C   LYS A  79 "
        model="   5" pdb=" N   GLY A  80 "
        model="   5" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  139.01  -17.31 1.80e+00 3.09e-01 9.25e+01
  angle model="   5" pdb=" C   LYS A  79 "
        model="   5" pdb=" CA  LYS A  79 "
        model="   5" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.10   92.95   17.15 1.90e+00 2.77e-01 8.15e+01
  angle model="   5" pdb=" N   ILE A  78 "
        model="   5" pdb=" CA  ILE A  78 "
        model="   5" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.00   84.40   25.60 3.00e+00 1.11e-01 7.28e+01
  angle model="   5" pdb=" C   TYR A  89 "
        model="   5" pdb=" N   SER A  90 "
        model="   5" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  107.67   14.03 1.80e+00 3.09e-01 6.08e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 926
       17.14 -    34.28: 64
       34.28 -    51.42: 24
       51.42 -    68.56: 4
       68.56 -    85.70: 5
  Dihedral angle restraints: 1023
    sinusoidal: 562
      harmonic: 461
  Sorted by residual:
  dihedral model="   5" pdb=" CA  GLY A  80 "
           model="   5" pdb=" C   GLY A  80 "
           model="   5" pdb=" N   TYR A  81 "
           model="   5" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  -94.30  -85.70     0      5.00e+00 4.00e-02 2.94e+02
  dihedral model="   5" pdb=" CA  SER A  90 "
           model="   5" pdb=" C   SER A  90 "
           model="   5" pdb=" N   TYR A  91 "
           model="   5" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -95.83  -84.17     0      5.00e+00 4.00e-02 2.83e+02
  dihedral model="   5" pdb=" CA  TYR A  89 "
           model="   5" pdb=" C   TYR A  89 "
           model="   5" pdb=" N   SER A  90 "
           model="   5" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -96.98  -83.02     0      5.00e+00 4.00e-02 2.76e+02
  ... (remaining 1020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.129: 169
       1.129 -    2.258: 0
       2.258 -    3.387: 1
       3.387 -    4.516: 2
       4.516 -    5.645: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CA  LYS A  79 "
            model="   5" pdb=" N   LYS A  79 "
            model="   5" pdb=" C   LYS A  79 "
            model="   5" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.13    5.65 2.00e-01 2.50e+01 7.97e+02
  chirality model="   5" pdb=" CB  ILE A  78 "
            model="   5" pdb=" CA  ILE A  78 "
            model="   5" pdb=" CG1 ILE A  78 "
            model="   5" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.71    5.35 2.00e-01 2.50e+01 7.16e+02
  chirality model="   5" pdb=" CB  ILE A 131 "
            model="   5" pdb=" CA  ILE A 131 "
            model="   5" pdb=" CG1 ILE A 131 "
            model="   5" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.49    5.13 2.00e-01 2.50e+01 6.58e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  91 "    0.806 2.00e-02 2.50e+03   3.06e-01 2.80e+03
        model="   5" pdb=" CG  TYR A  91 "   -0.058 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  91 "   -0.206 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  91 "   -0.152 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  91 "   -0.019 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  91 "   -0.063 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  91 "    0.092 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  91 "    0.361 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  91 "   -0.418 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  91 "   -0.272 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  91 "    0.034 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  91 "   -0.105 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  50 "   -0.169 2.00e-02 2.50e+03   6.72e-02 1.36e+02
        model="   5" pdb=" CG  TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  50 "    0.035 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  50 "    0.041 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  50 "   -0.114 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  50 "    0.049 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  50 "    0.069 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  50 "    0.030 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  50 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  HIS A  43 "    0.113 2.00e-02 2.50e+03   6.63e-02 8.79e+01
        model="   5" pdb=" CG  HIS A  43 "   -0.090 2.00e-02 2.50e+03
        model="   5" pdb=" ND1 HIS A  43 "   -0.085 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 HIS A  43 "   -0.022 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 HIS A  43 "    0.012 2.00e-02 2.50e+03
        model="   5" pdb=" NE2 HIS A  43 "    0.062 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 HIS A  43 "   -0.031 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 HIS A  43 "    0.041 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 104
        2.12 -     2.74: 3866
        2.74 -     3.36: 6325
        3.36 -     3.98: 7805
        3.98 -     4.60: 11639
  Nonbonded interactions: 29739
  Sorted by model distance:
  nonbonded model="   5" pdb=" HA  ILE A  77 "
            model="   5" pdb=" HA  ILE A  78 "
     model   vdw
     1.505 2.440
  nonbonded model="   5" pdb="HD12 ILE A  78 "
            model="   5" pdb=" H   TYR A  81 "
     model   vdw
     1.632 2.270
  nonbonded model="   5" pdb=" OD1 ASP A  95 "
            model="   5" pdb=" HG  SER A  97 "
     model   vdw
     1.734 1.850
  nonbonded model="   5" pdb=" O   LYS A  79 "
            model="   5" pdb=" HG1 THR A  82 "
     model   vdw
     1.781 1.850
  nonbonded model="   5" pdb=" OD1 ASP A  44 "
            model="   5" pdb=" HG  SER A  46 "
     model   vdw
     1.798 1.850
  ... (remaining 29734 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.09 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 463
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   8" pdb=" N   MET A   1 "
       model="   8" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.44e+00
  bond model="   8" pdb=" NE  ARG A 129 "
       model="   8" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 7.20e-02
  bond model="   8" pdb=" CZ  ARG A 127 "
       model="   8" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 6.36e-02
  bond model="   8" pdb=" NE  ARG A  21 "
       model="   8" pdb=" CZ  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 5.57e-02
  bond model="   8" pdb=" CZ  ARG A 129 "
       model="   8" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 5.41e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.88 -   106.88: 66
      106.88 -   112.88: 2719
      112.88 -   118.88: 426
      118.88 -   124.87: 824
      124.87 -   130.87: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   8" pdb=" CB  PRO A  54 "
        model="   8" pdb=" CA  PRO A  54 "
        model="   8" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.85   -4.85 3.00e+00 1.11e-01 2.61e+00
  angle model="   8" pdb=" CB  PRO A 117 "
        model="   8" pdb=" CA  PRO A 117 "
        model="   8" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.84   -4.84 3.00e+00 1.11e-01 2.61e+00
  angle model="   8" pdb=" CB  PRO A 102 "
        model="   8" pdb=" CA  PRO A 102 "
        model="   8" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  113.82   -4.82 3.00e+00 1.11e-01 2.58e+00
  angle model="   8" pdb=" CB  PRO A   6 "
        model="   8" pdb=" CA  PRO A   6 "
        model="   8" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   8" pdb=" CB  PRO A 114 "
        model="   8" pdb=" CA  PRO A 114 "
        model="   8" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.79   -4.79 3.00e+00 1.11e-01 2.55e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 874
       16.99 -    33.98: 80
       33.98 -    50.97: 52
       50.97 -    67.95: 21
       67.95 -    84.94: 5
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   8" pdb=" CB  GLU A  16 "
           model="   8" pdb=" CG  GLU A  16 "
           model="   8" pdb=" CD  GLU A  16 "
           model="   8" pdb=" OE1 GLU A  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.94   84.94     1      3.00e+01 1.11e-03 9.73e+00
  dihedral model="   8" pdb=" N   GLU A   8 "
           model="   8" pdb=" CA  GLU A   8 "
           model="   8" pdb=" CB  GLU A   8 "
           model="   8" pdb=" CG  GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.90  -59.10     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   8" pdb=" CA  LYS A  79 "
           model="   8" pdb=" CB  LYS A  79 "
           model="   8" pdb=" CG  LYS A  79 "
           model="   8" pdb=" CD  LYS A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.96  -59.04     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.020: 115
       0.020 -    0.038: 38
       0.038 -    0.057: 4
       0.057 -    0.076: 0
       0.076 -    0.095: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   8" pdb=" CA  ILE A  78 "
            model="   8" pdb=" N   ILE A  78 "
            model="   8" pdb=" C   ILE A  78 "
            model="   8" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.24e-01
  chirality model="   8" pdb=" CA  ILE A  38 "
            model="   8" pdb=" N   ILE A  38 "
            model="   8" pdb=" C   ILE A  38 "
            model="   8" pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.16e-01
  chirality model="   8" pdb=" CA  ILE A 131 "
            model="   8" pdb=" N   ILE A 131 "
            model="   8" pdb=" C   ILE A 131 "
            model="   8" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.14e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  PHE A  67 "   -0.000 2.00e-02 2.50e+03   1.07e-03 3.46e-02
        model="   8" pdb=" CG  PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 PHE A  67 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 PHE A  67 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 PHE A  67 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 PHE A  67 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HZ  PHE A  67 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  PHE A  15 "    0.000 2.00e-02 2.50e+03   1.04e-03 3.26e-02
        model="   8" pdb=" CG  PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 PHE A  15 "    0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HZ  PHE A  15 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   8" pdb=" CB  PHE A  45 "   -0.000 2.00e-02 2.50e+03   9.85e-04 2.91e-02
        model="   8" pdb=" CG  PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CE1 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   8" pdb=" CE2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   8" pdb=" CZ  PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD1 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HD2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   8" pdb=" HE1 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HE2 PHE A  45 "   -0.002 2.00e-02 2.50e+03
        model="   8" pdb=" HZ  PHE A  45 "    0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.06: 61
        2.06 -     2.70: 3708
        2.70 -     3.33: 6249
        3.33 -     3.97: 7546
        3.97 -     4.60: 11142
  Nonbonded interactions: 28706
  Sorted by model distance:
  nonbonded model="   8" pdb="HD13 LEU A   3 "
            model="   8" pdb="HD22 LEU A  53 "
     model   vdw
     1.428 2.440
  nonbonded model="   8" pdb="HD23 LEU A   9 "
            model="   8" pdb="HD22 LEU A  26 "
     model   vdw
     1.455 2.440
  nonbonded model="   8" pdb="HG23 ILE A  37 "
            model="   8" pdb="HG21 ILE A 108 "
     model   vdw
     1.605 2.440
  nonbonded model="   8" pdb="HD23 LEU A   2 "
            model="   8" pdb=" HB  THR A  34 "
     model   vdw
     1.737 2.440
  nonbonded model="   8" pdb="HG22 VAL A  18 "
            model="   8" pdb=" HB3 ALA A  69 "
     model   vdw
     1.745 2.440
  ... (remaining 28701 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   7" pdb=" CB  ILE A  51 "
        model="   7" pdb=" CB  PRO A  52 "
        model="   7" pdb=" CB  ILE A  77 "
        model="   7" pdb=" CB  TYR A  89 "
        model="   7" pdb=" CB  LYS A 125 "
        model="   7" pdb=" CB  MET A 128 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 0.98 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 60
        1.23 -     1.43: 413
        1.43 -     1.62: 659
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   7" pdb=" N   GLY A  80 "
       model="   7" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.587 -0.136 1.60e-02 3.91e+03 7.18e+01
  bond model="   7" pdb=" CA  ASP A  88 "
       model="   7" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.613 -0.088 2.10e-02 2.27e+03 1.76e+01
  bond model="   7" pdb=" CA  GLY A 121 "
       model="   7" pdb=" C   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.516  1.587 -0.071 1.80e-02 3.09e+03 1.55e+01
  bond model="   7" pdb=" N   ILE A 122 "
       model="   7" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.531 -0.073 1.90e-02 2.77e+03 1.49e+01
  bond model="   7" pdb=" CA  GLY A  80 "
       model="   7" pdb=" C   GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.516  1.448  0.068 1.80e-02 3.09e+03 1.44e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       80.26 -    91.72: 2
       91.72 -   103.17: 44
      103.17 -   114.63: 2853
      114.63 -   126.09: 1120
      126.09 -   137.55: 60
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   7" pdb=" C   LYS A 125 "
        model="   7" pdb=" CA  LYS A 125 "
        model="   7" pdb=" CB  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     110.10  129.17  -19.07 1.90e+00 2.77e-01 1.01e+02
  angle model="   7" pdb=" C   TYR A  81 "
        model="   7" pdb=" CA  TYR A  81 "
        model="   7" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     109.00   80.26   28.74 3.00e+00 1.11e-01 9.18e+01
  angle model="   7" pdb=" C   LYS A  79 "
        model="   7" pdb=" N   GLY A  80 "
        model="   7" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  137.55  -15.85 1.80e+00 3.09e-01 7.75e+01
  angle model="   7" pdb=" C   ALA A 124 "
        model="   7" pdb=" N   LYS A 125 "
        model="   7" pdb=" CA  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     121.70  137.40  -15.70 1.80e+00 3.09e-01 7.61e+01
  angle model="   7" pdb=" N   TYR A  91 "
        model="   7" pdb=" CA  TYR A  91 "
        model="   7" pdb=" CB  TYR A  91 "
      ideal   model   delta    sigma   weight residual
     110.50  124.86  -14.36 1.70e+00 3.46e-01 7.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.03: 952
       26.03 -    52.07: 59
       52.07 -    78.10: 5
       78.10 -   104.14: 4
      104.14 -   130.17: 1
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   7" pdb=" CA  LYS A 125 "
           model="   7" pdb=" C   LYS A 125 "
           model="   7" pdb=" N   VAL A 126 "
           model="   7" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   49.83  130.17     0      5.00e+00 4.00e-02 6.78e+02
  dihedral model="   7" pdb=" CA  ILE A  77 "
           model="   7" pdb=" C   ILE A  77 "
           model="   7" pdb=" N   ILE A  78 "
           model="   7" pdb=" CA  ILE A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   76.84  103.16     0      5.00e+00 4.00e-02 4.26e+02
  dihedral model="   7" pdb=" C   TYR A  81 "
           model="   7" pdb=" N   TYR A  81 "
           model="   7" pdb=" CA  TYR A  81 "
           model="   7" pdb=" CB  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -167.61   45.01     0      2.50e+00 1.60e-01 3.24e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.081: 167
       1.081 -    2.160: 2
       2.160 -    3.240: 0
       3.240 -    4.320: 0
       4.320 -    5.400: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   7" pdb=" CA  ILE A  77 "
            model="   7" pdb=" N   ILE A  77 "
            model="   7" pdb=" C   ILE A  77 "
            model="   7" pdb=" CB  ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -2.97    5.40 2.00e-01 2.50e+01 7.29e+02
  chirality model="   7" pdb=" CA  PRO A  52 "
            model="   7" pdb=" N   PRO A  52 "
            model="   7" pdb=" C   PRO A  52 "
            model="   7" pdb=" CB  PRO A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72   -2.39    5.11 2.00e-01 2.50e+01 6.53e+02
  chirality model="   7" pdb=" CA  MET A 128 "
            model="   7" pdb=" N   MET A 128 "
            model="   7" pdb=" C   MET A 128 "
            model="   7" pdb=" CB  MET A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.54    5.05 2.00e-01 2.50e+01 6.38e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  91 "   -0.169 2.00e-02 2.50e+03   8.05e-02 1.94e+02
        model="   7" pdb=" CG  TYR A  91 "   -0.031 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  91 "    0.023 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  91 "    0.044 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  91 "    0.032 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  91 "   -0.025 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  91 "   -0.148 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  91 "    0.052 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  91 "    0.116 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  91 "    0.076 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  91 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CB  TYR A  50 "   -0.160 2.00e-02 2.50e+03   6.82e-02 1.39e+02
        model="   7" pdb=" CG  TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   7" pdb=" CD1 TYR A  50 "    0.034 2.00e-02 2.50e+03
        model="   7" pdb=" CD2 TYR A  50 "    0.034 2.00e-02 2.50e+03
        model="   7" pdb=" CE1 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   7" pdb=" CE2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   7" pdb=" CZ  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   7" pdb=" OH  TYR A  50 "   -0.138 2.00e-02 2.50e+03
        model="   7" pdb=" HD1 TYR A  50 "    0.053 2.00e-02 2.50e+03
        model="   7" pdb=" HD2 TYR A  50 "    0.050 2.00e-02 2.50e+03
        model="   7" pdb=" HE1 TYR A  50 "    0.031 2.00e-02 2.50e+03
        model="   7" pdb=" HE2 TYR A  50 "    0.033 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   7" pdb=" CA  LYS A 125 "    0.037 2.00e-02 2.50e+03   7.22e-02 5.22e+01
        model="   7" pdb=" C   LYS A 125 "   -0.125 2.00e-02 2.50e+03
        model="   7" pdb=" O   LYS A 125 "    0.045 2.00e-02 2.50e+03
        model="   7" pdb=" N   VAL A 126 "    0.043 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 184
        2.19 -     2.79: 4208
        2.79 -     3.39: 6464
        3.39 -     4.00: 7763
        4.00 -     4.60: 11508
  Nonbonded interactions: 30127
  Sorted by model distance:
  nonbonded model="   7" pdb=" HA  ILE A  77 "
            model="   7" pdb="HD12 ILE A  78 "
     model   vdw
     1.582 2.440
  nonbonded model="   7" pdb=" HB3 LYS A 125 "
            model="   7" pdb=" H   ARG A 127 "
     model   vdw
     1.657 2.270
  nonbonded model="   7" pdb="HD13 ILE A  78 "
            model="   7" pdb=" HA  LEU A  93 "
     model   vdw
     1.712 2.440
  nonbonded model="   7" pdb=" HG2 LYS A  79 "
            model="   7" pdb=" H   GLY A  80 "
     model   vdw
     1.712 2.270
  nonbonded model="   7" pdb="HG12 ILE A  78 "
            model="   7" pdb=" HB3 LEU A  93 "
     model   vdw
     1.716 2.440
  ... (remaining 30122 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.048 (Z=  2.957)
  Mean delta:    0.013 (Z=  0.656)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  75  GLU  CA
   A  75  GLU  C
   A  75  GLU  O         120.80   129.78    -8.98  1.70e+00  2.79e+01   5.3*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N         116.20   105.91    10.29  2.00e+00  2.65e+01   5.1*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   130.46    -8.76  1.80e+00  2.37e+01   4.9*sigma
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        121.70   113.33     8.37  1.80e+00  2.16e+01   4.6*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.25     4.35  1.00e+00  1.89e+01   4.4*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   129.30    -7.60  1.80e+00  1.78e+01   4.2*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   10.289 (Z=  5.283)
  Mean delta:    2.050 (Z=  1.103)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   107.74    72.26  5.00e+00  2.09e+02  14.5*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   127.71    52.29  5.00e+00  1.09e+02  10.5*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00  -129.77   -50.23  5.00e+00  1.01e+02  10.0*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   145.93    34.07  5.00e+00  4.64e+01   6.8*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   154.36    25.64  5.00e+00  2.63e+01   5.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   156.58    23.42  5.00e+00  2.19e+01   4.7*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   157.51    22.49  5.00e+00  2.02e+01   4.5*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   158.36    21.64  5.00e+00  1.87e+01   4.3*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   159.54    20.46  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.040
  Max. delta:   81.492
  Mean delta:   16.784

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  75  GLU  CA
   A  75  GLU  N
   A  75  GLU  C
   A  75  GLU  CB          2.51    -1.87     4.38  2.00e-01  4.80e+02  21.9*sigma

  Min. delta:    0.000
  Max. delta:    4.381
  Mean delta:    0.342

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  67  PHE  CB
   A  67  PHE  CG
   A  67  PHE  CD1
   A  67  PHE  CD2
   A  67  PHE  CE1
   A  67  PHE  CE2
   A  67  PHE  CZ            0.115       0.138      230.94   6.9*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.118       0.125      280.02   6.3*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.100       0.097      198.32   4.9*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.088       0.082      156.13   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.118
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  75  GLU  HA , Angle N-CA-HA, observed: 97.396, delta from target: 12.604

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.048   2242  Z= 0.467
    Angle     :  1.829  12.604   4079  Z= 0.809
    Chirality :  0.342   4.381    176
    Planarity :  0.017   0.146    327
    Dihedral  : 14.506  81.492    769
    Min Nonbonded Distance : 1.783
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  9.49 %
      Favored  : 86.13 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  : 10.48 %
      Favored  : 84.68 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 3.05 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.17 (0.59), residues: 137
    helix: -1.52 (0.51), residues: 61
    sheet:  None (None), residues: 0
    loop : -2.69 (0.64), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.040   0.007   HIS A  43 
   PHE   0.277   0.046   PHE A  67 
   TYR   0.299   0.044   TYR A  50 
   ARG   0.033   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.040   0.007   HIS A  43 
   PHE   0.176   0.044   PHE A  67 
   TYR   0.230   0.048   TYR A  50 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   4.38 %
                favored =  86.13 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     1
  Clashscore            =   8.57
  RMS(bonds)            =   0.0090
  RMS(angles)           =   1.83
  MolProbity score      =   2.62

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.792)
  Mean delta:    0.013 (Z=  0.685)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        121.70   131.84   -10.14  1.80e+00  3.17e+01   5.6*sigma
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        121.70   131.13    -9.43  1.80e+00  2.75e+01   5.2*sigma
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        121.70   130.67    -8.97  1.80e+00  2.48e+01   5.0*sigma
   A 135  HIS  CA
   A 135  HIS  CB
   A 135  HIS  CG        113.80   118.64    -4.84  1.00e+00  2.35e+01   4.8*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   117.31    -4.71  1.00e+00  2.22e+01   4.7*sigma
   A 134  HIS  N
   A 134  HIS  CA
   A 134  HIS  C         111.00   124.03   -13.03  2.80e+00  2.17e+01   4.7*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.39     5.81  1.30e+00  1.99e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.23     4.37  1.00e+00  1.91e+01   4.4*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.67     5.53  1.30e+00  1.81e+01   4.3*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N         116.20   107.89     8.31  2.00e+00  1.73e+01   4.2*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 134  HIS  O         120.80   127.80    -7.00  1.70e+00  1.69e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   13.029 (Z=  5.633)
  Mean delta:    2.095 (Z=  1.135)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   148.59    31.41  5.00e+00  3.95e+01   6.3*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   157.47    22.53  5.00e+00  2.03e+01   4.5*sigma
   A   3  LEU  CA
   A   3  LEU  C
   A   4  ILE  N
   A   4  ILE  CA        180.00   159.27    20.73  5.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.022
  Max. delta:   84.903
  Mean delta:   17.939

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 134  HIS  CA
   A 134  HIS  N
   A 134  HIS  C
   A 134  HIS  CB          2.51    -1.87     4.38  2.00e-01  4.79e+02  21.9*sigma
   A   3  LEU  CA
   A   3  LEU  N
   A   3  LEU  C
   A   3  LEU  CB          2.51    -1.85     4.36  2.00e-01  4.75e+02  21.8*sigma

  Min. delta:    0.000
  Max. delta:    4.378
  Mean delta:    0.475

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.082       0.142      134.92   7.1*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  ND1
   A 134  HIS  CD2
   A 134  HIS  CE1
   A 134  HIS  NE2           0.097       0.129      140.22   6.4*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.092       0.104      168.00   5.2*sigma

  Min. delta:    0.000
  Max. delta:    0.097
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 134  HIS  HA , Angle N-CA-HA, observed: 97.532, delta from target: 12.468
   A   3  LEU  HA , Angle N-CA-HA, observed: 96.348, delta from target: 13.652

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.487
    Angle     :  1.888  13.652   4079  Z= 0.836
    Chirality :  0.475   4.378    176
    Planarity :  0.015   0.106    327
    Dihedral  : 14.823  84.903    769
    Min Nonbonded Distance : 1.636
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  9.49 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  9.68 %
      Allowed  :  3.23 %
      Favored  : 87.10 %
    Cbeta Deviations :  2.27 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.92 (0.60), residues: 137
    helix: -1.80 (0.48), residues: 68
    sheet:  None (None), residues: 0
    loop : -2.04 (0.71), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.025   0.005   HIS A 134 
   PHE   0.130   0.024   PHE A  45 
   TYR   0.187   0.034   TYR A  89 
   ARG   0.073   0.018   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.025   0.005   HIS A 134 
   PHE   0.079   0.020   PHE A  45 
   TYR   0.150   0.034   TYR A  89 
   ARG   0.011   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.930)
  Mean delta:    0.013 (Z=  0.656)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   108.09     4.51  1.00e+00  2.04e+01   4.5*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.29     4.31  1.00e+00  1.86e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.29     4.31  1.00e+00  1.86e+01   4.3*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.67     5.53  1.30e+00  1.81e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.126 (Z=  4.514)
  Mean delta:    1.828 (Z=  0.998)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   157.78    22.22  5.00e+00  1.98e+01   4.4*sigma

  Min. delta:    0.014
  Max. delta:   82.924
  Mean delta:   19.281

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.267
  Mean delta:    0.090

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  ND1
   A  43  HIS  CD2
   A  43  HIS  CE1
   A  43  HIS  NE2           0.075       0.100       84.12   5.0*sigma

  Min. delta:    0.000
  Max. delta:    0.091
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.467
    Angle     :  1.683   8.126   4079  Z= 0.742
    Chirality :  0.090   0.267    176
    Planarity :  0.013   0.081    327
    Dihedral  : 15.456  82.924    769
    Min Nonbonded Distance : 1.835
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  4.38 %
      Favored  : 94.16 %
    Rotamer:
      Outliers : 10.48 %
      Allowed  :  7.26 %
      Favored  : 82.26 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.11 (0.70), residues: 137
    helix: -0.04 (0.48), residues: 73
    sheet:  None (None), residues: 0
    loop : -1.54 (0.92), residues: 64
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.050   0.014   PHE A  45 
   TYR   0.153   0.028   TYR A  81 
   ARG   0.078   0.018   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.023   0.008   PHE A  45 
   TYR   0.127   0.028   TYR A  81 
   ARG   0.006   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  94.16 %
  Rotamer outliers      =  10.48 %
  C-beta deviations     =     1
  Clashscore            =   1.80
  RMS(bonds)            =   0.0090
  RMS(angles)           =   1.68
  MolProbity score      =   2.11

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.19 %
                favored =  88.32 %
  Rotamer outliers      =   9.68 %
  C-beta deviations     =     3
  Clashscore            =   4.51
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.89
  MolProbity score      =   2.57

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.69    -0.23  1.60e-02  2.15e+02  14.7*sigma
   A  77  ILE  N
   A  77  ILE  CA          1.46     1.71    -0.26  1.90e-02  1.81e+02  13.4*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.67    -0.21  1.90e-02  1.21e+02  11.0*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.75    -0.23  2.10e-02  1.17e+02  10.8*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.74    -0.22  2.10e-02  1.05e+02  10.2*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.45    -0.12  1.40e-02  7.18e+01   8.5*sigma
   A  79  LYS  C
   A  80  GLY  N           1.33     1.44    -0.11  1.40e-02  5.90e+01   7.7*sigma
   A  76  SER  C
   A  77  ILE  N           1.33     1.43    -0.10  1.40e-02  4.74e+01   6.9*sigma
   A  77  ILE  CA
   A  77  ILE  CB          1.54     1.72    -0.18  2.70e-02  4.56e+01   6.8*sigma
   A  76  SER  CA
   A  76  SER  C           1.52     1.64    -0.11  2.10e-02  3.00e+01   5.5*sigma
   A  77  ILE  C
   A  78  ILE  N           1.33     1.26     0.07  1.40e-02  2.59e+01   5.1*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.255 (Z= 14.669)
  Mean delta:    0.023 (Z=  1.235)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   141.64   -31.14  1.70e+00  3.36e+02  18.3*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   153.13   -31.43  1.80e+00  3.05e+02  17.5*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   147.67   -25.97  1.80e+00  2.08e+02  14.4*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   147.15   -25.45  1.80e+00  2.00e+02  14.1*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   135.00   -23.50  1.70e+00  1.91e+02  13.8*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   131.66   -21.56  1.90e+00  1.29e+02  11.3*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   136.66   -20.46  2.00e+00  1.05e+02  10.2*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   127.44   -16.94  1.70e+00  9.93e+01  10.0*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50    96.00    15.50  1.70e+00  8.31e+01   9.1*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   108.99    14.01  1.60e+00  7.66e+01   8.8*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N         116.20   132.60   -16.40  2.00e+00  6.72e+01   8.2*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   136.03   -14.33  1.80e+00  6.34e+01   8.0*sigma
   A  76  SER  C
   A  76  SER  CA
   A  76  SER  CB        110.10   125.21   -15.11  1.90e+00  6.32e+01   8.0*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00    89.06    21.94  2.80e+00  6.14e+01   7.8*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   132.60   -21.60  2.80e+00  5.95e+01   7.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   131.54   -15.34  2.00e+00  5.88e+01   7.7*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00   131.92   -20.92  2.80e+00  5.58e+01   7.5*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   123.93   -13.83  1.90e+00  5.30e+01   7.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.71   -10.81  1.50e+00  5.20e+01   7.2*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   101.89    14.31  2.00e+00  5.12e+01   7.2*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   134.35   -12.65  1.80e+00  4.94e+01   7.0*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   111.97    11.03  1.60e+00  4.75e+01   6.9*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   106.12     6.48  1.00e+00  4.20e+01   6.5*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   126.30   -12.20  2.00e+00  3.72e+01   6.1*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   104.10    12.10  2.00e+00  3.66e+01   6.1*sigma
   A  77  ILE  CB
   A  77  ILE  CG1
   A  77  ILE  CD1       113.80   126.12   -12.32  2.10e+00  3.44e+01   5.9*sigma
   A  76  SER  O
   A  76  SER  C
   A  77  ILE  N         123.00   113.68     9.32  1.60e+00  3.39e+01   5.8*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG1       110.40   120.11    -9.71  1.70e+00  3.26e+01   5.7*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.72   -10.02  1.80e+00  3.10e+01   5.6*sigma
   A  77  ILE  CG1
   A  77  ILE  CB
   A  77  ILE  CG2       110.70    94.31    16.39  3.00e+00  2.99e+01   5.5*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.28    -9.58  1.80e+00  2.83e+01   5.3*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  C         111.00    96.20    14.80  2.80e+00  2.80e+01   5.3*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   123.45   -12.15  2.30e+00  2.79e+01   5.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  76  SER  O         120.80   112.13     8.67  1.70e+00  2.60e+01   5.1*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   130.65    -8.95  1.80e+00  2.47e+01   5.0*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   102.10     8.40  1.70e+00  2.44e+01   4.9*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O         120.80   112.46     8.34  1.70e+00  2.41e+01   4.9*sigma
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        121.70   112.96     8.74  1.80e+00  2.36e+01   4.9*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   116.88    -7.28  1.50e+00  2.35e+01   4.9*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   113.00     8.70  1.80e+00  2.34e+01   4.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   106.66     9.54  2.00e+00  2.27e+01   4.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O         120.80   128.74    -7.94  1.70e+00  2.18e+01   4.7*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.27     5.93  1.30e+00  2.08e+01   4.6*sigma
   A  97  SER  O
   A  97  SER  C
   A  98  SER  N         123.00   130.29    -7.29  1.60e+00  2.08e+01   4.6*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.28     5.92  1.30e+00  2.07e+01   4.6*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   115.75     7.25  1.60e+00  2.06e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.07     4.53  1.00e+00  2.06e+01   4.5*sigma
   A  93  LEU  CA
   A  93  LEU  CB
   A  93  LEU  CG        116.30   132.03   -15.73  3.50e+00  2.02e+01   4.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   125.14    -8.94  2.00e+00  2.00e+01   4.5*sigma
   A 114  PRO  CA
   A 114  PRO  N
   A 114  PRO  CD        112.00   105.77     6.23  1.40e+00  1.98e+01   4.4*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   103.06     7.44  1.70e+00  1.91e+01   4.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 122  ILE  O         120.80   128.13    -7.33  1.70e+00  1.86e+01   4.3*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   120.21    -8.61  2.00e+00  1.85e+01   4.3*sigma
   A  91  TYR  O
   A  91  TYR  C
   A  92  THR  N         123.00   116.20     6.80  1.60e+00  1.81e+01   4.3*sigma
   A 114  PRO  N
   A 114  PRO  CA
   A 114  PRO  CB        103.00   107.66    -4.66  1.10e+00  1.79e+01   4.2*sigma
   A  76  SER  N
   A  76  SER  CA
   A  76  SER  CB        110.50   117.58    -7.08  1.70e+00  1.73e+01   4.2*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   116.76    -4.16  1.00e+00  1.73e+01   4.2*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   104.49     7.01  1.70e+00  1.70e+01   4.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  97  SER  O         120.80   127.80    -7.00  1.70e+00  1.70e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.52     4.08  1.00e+00  1.66e+01   4.1*sigma
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        121.70   128.99    -7.29  1.80e+00  1.64e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.56     4.04  1.00e+00  1.63e+01   4.0*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00    99.70    11.30  2.80e+00  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   31.426 (Z= 18.320)
  Mean delta:    3.586 (Z=  1.903)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00    65.98   114.02  5.00e+00  5.20e+02  22.8*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -76.20  -103.80  5.00e+00  4.31e+02  20.8*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   -80.83   -99.17  5.00e+00  3.93e+02  19.8*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00    91.60    88.40  5.00e+00  3.13e+02  17.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   109.50    70.50  5.00e+00  1.99e+02  14.1*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00  -118.10   -61.90  5.00e+00  1.53e+02  12.4*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   121.64    58.36  5.00e+00  1.36e+02  11.7*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -126.23   -53.77  5.00e+00  1.16e+02  10.8*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   130.90    49.10  5.00e+00  9.64e+01   9.8*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   138.62    41.38  5.00e+00  6.85e+01   8.3*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   145.21    34.79  5.00e+00  4.84e+01   7.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -147.13   -32.87  5.00e+00  4.32e+01   6.6*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   148.50    31.50  5.00e+00  3.97e+01   6.3*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   148.94    31.06  5.00e+00  3.86e+01   6.2*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   150.79    29.21  5.00e+00  3.41e+01   5.8*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00   152.43    27.57  5.00e+00  3.04e+01   5.5*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   153.21    26.79  5.00e+00  2.87e+01   5.4*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00  -154.79   -25.21  5.00e+00  2.54e+01   5.0*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   156.04    23.96  5.00e+00  2.30e+01   4.8*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -157.49   -22.51  5.00e+00  2.03e+01   4.5*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA          0.00    21.01   -21.01  5.00e+00  1.77e+01   4.2*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   159.78    20.22  5.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.025
  Max. delta:  114.022
  Mean delta:   20.211

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.62     5.15  2.00e-01  6.62e+02  25.7*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.48     5.13  2.00e-01  6.57e+02  25.6*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.60     5.11  2.00e-01  6.53e+02  25.6*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.32     4.87  2.00e-01  5.93e+02  24.4*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.26     4.77  2.00e-01  5.70e+02  23.9*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -1.78     4.29  2.00e-01  4.61e+02  21.5*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.16     3.67  2.00e-01  3.36e+02  18.3*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.91     3.35  2.00e-01  2.80e+02  16.7*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43     0.03     2.41  2.00e-01  1.45e+02  12.0*sigma
   A  76  SER  CA
   A  76  SER  N
   A  76  SER  C
   A  76  SER  CB          2.51     0.72     1.79  2.00e-01  8.02e+01   9.0*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64     1.55     1.10  2.00e-01  3.01e+01   5.5*sigma

  Min. delta:    0.001
  Max. delta:    5.148
  Mean delta:    1.020

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.137       0.235      374.68  11.8*sigma
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.075       0.135      113.11   6.8*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O
   A  78  ILE  N             0.049       0.085       24.09   4.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O
   A  80  GLY  N             0.049       0.085       23.90   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.137
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  80  GLY  H  , Angle CA-N-H, observed: 101.929, delta from target: 12.071
   A  51  ILE  HA , Angle CB-CA-HA, observed: 95.547, delta from target: 13.453
   A  77  ILE  H  , Angle C-N-H, observed: 110.686, delta from target: 13.614
   A  80  GLY  H  , Angle C-N-H, observed: 110.397, delta from target: 13.903
   A  93  LEU  HA , Angle CB-CA-HA, observed: 94.713, delta from target: 14.287
   A  92  THR  HA , Angle CB-CA-HA, observed: 123.424, delta from target: -14.424
   A  71  ILE  HB , Angle CA-CB-HB, observed: 94.332, delta from target: 14.668
   A  93  LEU  HA , Angle N-CA-HA, observed: 95.325, delta from target: 14.675
   A  79  LYS  H  , Angle CA-N-H, observed: 99.296, delta from target: 14.704
   A  89  TYR  HA , Angle N-CA-HA, observed: 126.188, delta from target: -16.188
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.489, delta from target: 16.511
   A  79  LYS  H  , Angle C-N-H, observed: 107.579, delta from target: 16.721
   A  79  LYS  HA , Angle CB-CA-HA, observed: 125.980, delta from target: -16.980
   A  76  SER  HA , Angle C-CA-HA, observed: 88.430, delta from target: 20.570
   A  89  TYR  HA , Angle CB-CA-HA, observed: 87.986, delta from target: 21.014
   A  79  LYS  HA , Angle C-CA-HA, observed: 86.518, delta from target: 22.482
   A  77  ILE  HA , Angle CB-CA-HA, observed: 85.070, delta from target: 23.930
   A  77  ILE  HA , Angle C-CA-HA, observed: 133.551, delta from target: -24.551
   A  89  TYR  HA , Angle C-CA-HA, observed: 84.127, delta from target: 24.873
   A  76  SER  HA , Angle CB-CA-HA, observed: 80.786, delta from target: 28.214
   A  77  ILE  HB , Angle CG1-CB-HB, observed: 140.023, delta from target: -31.023
   A  78  ILE  HA , Angle N-CA-HA, observed: 77.171, delta from target: 32.829
   A  77  ILE  HB , Angle CA-CB-HB, observed: 68.965, delta from target: 40.035
   A  78  ILE  HA , Angle C-CA-HA, observed: 55.487, delta from target: 53.513
   A  78  ILE  HA , Angle CB-CA-HA, observed: 171.036, delta from target: -62.036

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.017   0.255   2242  Z= 0.879
    Angle     :  3.405  62.036   4079  Z= 1.455
    Chirality :  1.020   5.148    176
    Planarity :  0.016   0.153    327
    Dihedral  : 16.714 114.022    769
    Min Nonbonded Distance : 1.293
  
  Molprobity Statistics.
    All-atom Clashscore : 33.81
    Ramachandran Plot:
      Outliers :  8.76 %
      Allowed  :  8.03 %
      Favored  : 83.21 %
    Rotamer:
      Outliers :  9.68 %
      Allowed  :  8.87 %
      Favored  : 81.45 %
    Cbeta Deviations :  9.85 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 1.53 %
      Twisted Proline : 14.29 %
      Twisted General : 9.92 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.37 (0.61), residues: 137
    helix: -2.47 (0.52), residues: 61
    sheet:  None (None), residues: 0
    loop : -3.40 (0.66), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A 138 
   PHE   0.082   0.017   PHE A  15 
   TYR   0.284   0.033   TYR A  91 
   ARG   0.058   0.007   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.004   HIS A 138 
   PHE   0.055   0.015   PHE A  15 
   TYR   0.235   0.038   TYR A  91 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   8.76 %
                favored =  83.21 %
  Rotamer outliers      =   9.68 %
  C-beta deviations     =    13
  Clashscore            =  33.81
  RMS(bonds)            =   0.0166
  RMS(angles)           =   3.41
  MolProbity score      =   3.45

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  92  THR  C
   A  93  LEU  N           1.33     1.26     0.07  1.40e-02  2.31e+01   4.8*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.074 (Z=  4.807)
  Mean delta:    0.016 (Z=  0.812)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   140.53   -18.83  1.80e+00  1.09e+02  10.5*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   138.67   -16.97  1.80e+00  8.88e+01   9.4*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50    95.45    15.05  1.70e+00  7.84e+01   8.9*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   124.16   -14.06  1.90e+00  5.48e+01   7.4*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   101.67    14.53  2.00e+00  5.28e+01   7.3*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   102.58    13.62  2.00e+00  4.64e+01   6.8*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   133.72   -12.02  1.80e+00  4.46e+01   6.7*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   124.46   -12.86  2.00e+00  4.14e+01   6.4*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   122.21   -12.11  1.90e+00  4.06e+01   6.4*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   121.23   -10.73  1.70e+00  3.98e+01   6.3*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.67    -6.07  1.00e+00  3.69e+01   6.1*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   132.37   -10.67  1.80e+00  3.51e+01   5.9*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   101.83     9.67  1.70e+00  3.24e+01   5.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.93   -10.23  1.80e+00  3.23e+01   5.7*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    95.40    15.60  2.80e+00  3.10e+01   5.6*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30    98.41    10.89  2.00e+00  2.97e+01   5.4*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   131.40    -9.70  1.80e+00  2.90e+01   5.4*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   131.34    -9.64  1.80e+00  2.87e+01   5.4*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N         116.20   105.51    10.69  2.00e+00  2.86e+01   5.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   124.71    -7.81  1.50e+00  2.71e+01   5.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   126.14    -9.94  2.00e+00  2.47e+01   5.0*sigma
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        121.70   130.57    -8.87  1.80e+00  2.43e+01   4.9*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O         120.80   128.88    -8.08  1.70e+00  2.26e+01   4.8*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   129.91    -8.21  1.80e+00  2.08e+01   4.6*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  C         111.00   123.66   -12.66  2.80e+00  2.04e+01   4.5*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   115.90     7.10  1.60e+00  1.97e+01   4.4*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG1       110.40   117.93    -7.53  1.70e+00  1.96e+01   4.4*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   129.62    -7.92  1.80e+00  1.94e+01   4.4*sigma
   A 128  MET  CA
   A 128  MET  CB
   A 128  MET  CG        114.10   105.34     8.76  2.00e+00  1.92e+01   4.4*sigma
   A  39  LEU  N
   A  39  LEU  CA
   A  39  LEU  CB        110.50   103.23     7.27  1.70e+00  1.83e+01   4.3*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50   104.36     7.14  1.70e+00  1.76e+01   4.2*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   116.78    -4.18  1.00e+00  1.75e+01   4.2*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   117.61    -7.11  1.70e+00  1.75e+01   4.2*sigma
   A  97  SER  O
   A  97  SER  C
   A  98  SER  N         123.00   129.67    -6.67  1.60e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   117.38    -6.98  1.70e+00  1.68e+01   4.1*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   108.08     8.12  2.00e+00  1.65e+01   4.1*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   117.82    -4.02  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   18.835 (Z= 10.464)
  Mean delta:    2.801 (Z=  1.503)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00    59.93   120.07  5.00e+00  5.77e+02  24.0*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    78.61   101.39  5.00e+00  4.11e+02  20.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    83.79    96.21  5.00e+00  3.70e+02  19.2*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   109.34    70.66  5.00e+00  2.00e+02  14.1*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   112.54    67.46  5.00e+00  1.82e+02  13.5*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -115.47   -64.53  5.00e+00  1.67e+02  12.9*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -118.45   -61.55  5.00e+00  1.52e+02  12.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -121.27   -58.73  5.00e+00  1.38e+02  11.7*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   121.34    58.66  5.00e+00  1.38e+02  11.7*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   128.73    51.27  5.00e+00  1.05e+02  10.3*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -131.91   -48.09  5.00e+00  9.25e+01   9.6*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -137.62   -42.38  5.00e+00  7.18e+01   8.5*sigma
   A  71  ILE  CA
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        180.00  -142.68   -37.32  5.00e+00  5.57e+01   7.5*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   147.82    32.18  5.00e+00  4.14e+01   6.4*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   149.27    30.73  5.00e+00  3.78e+01   6.1*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -149.41   -30.59  5.00e+00  3.74e+01   6.1*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -149.60   -30.40  5.00e+00  3.70e+01   6.1*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   149.62    30.38  5.00e+00  3.69e+01   6.1*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   150.86    29.14  5.00e+00  3.40e+01   5.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   151.47    28.53  5.00e+00  3.26e+01   5.7*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   156.37    23.63  5.00e+00  2.23e+01   4.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   156.43    23.57  5.00e+00  2.22e+01   4.7*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00  -157.34   -22.66  5.00e+00  2.05e+01   4.5*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   157.41    22.59  5.00e+00  2.04e+01   4.5*sigma
   A  91  TYR  CD1
   A  91  TYR  CE1
   A  91  TYR  CZ
   A  91  TYR  OH        180.00   158.63    21.37  5.00e+00  1.83e+01   4.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   158.98    21.02  5.00e+00  1.77e+01   4.2*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   159.56    20.44  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.025
  Max. delta:  120.066
  Mean delta:   19.762

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.18     5.69  2.00e-01  8.10e+02  28.5*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.83     5.34  2.00e-01  7.13e+02  26.7*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -2.81     5.32  2.00e-01  7.08e+02  26.6*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.57     5.22  2.00e-01  6.80e+02  26.1*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.77     5.20  2.00e-01  6.76e+02  26.0*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.51     5.02  2.00e-01  6.29e+02  25.1*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.47     5.00  2.00e-01  6.25e+02  25.0*sigma
   A 116  ASP  CA
   A 116  ASP  N
   A 116  ASP  C
   A 116  ASP  CB          2.51    -2.21     4.72  2.00e-01  5.57e+02  23.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.07     3.50  2.00e-01  3.06e+02  17.5*sigma
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51     1.11     1.40  2.00e-01  4.92e+01   7.0*sigma

  Min. delta:    0.003
  Max. delta:    5.694
  Mean delta:    1.153

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.210       0.365      880.11  18.2*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.063       0.118       80.40   5.9*sigma
   A  67  PHE  CB
   A  67  PHE  CG
   A  67  PHE  CD1
   A  67  PHE  CD2
   A  67  PHE  CE1
   A  67  PHE  CE2
   A  67  PHE  CZ            0.061       0.091       65.82   4.6*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.050       0.087       49.06   4.4*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 118  ASP  O
   A 119  LEU  N             0.050       0.086       24.68   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.210
  Mean delta:    0.022

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    3" pdbres="HIS A  43  conformer  : HE2, HD1 
    3" pdbres="LEU A  93  conformer  : H 
    3" pdbres="HIS A 134  conformer  : HE2, HD1 
    3" pdbres="HIS A 135  conformer  : HE2, HD1 
    3" pdbres="HIS A 136  conformer  : HE2, HD1 
    3" pdbres="HIS A 137  conformer  : HE2, HD1 
    3" pdbres="HIS A 138  conformer  : HE2, HD1 
    3" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  92  THR  HA , Angle N-CA-HA, observed: 97.801, delta from target: 12.199
   A 116  ASP  HA , Angle C-CA-HA, observed: 96.532, delta from target: 12.468
   A  92  THR  HA , Angle CB-CA-HA, observed: 121.521, delta from target: -12.521
   A  79  LYS  HA , Angle C-CA-HA, observed: 123.042, delta from target: -14.042
   A  99  LEU  HA , Angle CB-CA-HA, observed: 94.475, delta from target: 14.525
   A  93  LEU  HA , Angle CB-CA-HA, observed: 124.551, delta from target: -15.551
   A  51  ILE  HA , Angle CB-CA-HA, observed: 90.171, delta from target: 18.829
   A  51  ILE  HA , Angle C-CA-HA, observed: 89.741, delta from target: 19.259
   A  99  LEU  HA , Angle C-CA-HA, observed: 89.141, delta from target: 19.859

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.074   2241  Z= 0.578
    Angle     :  2.439  19.859   4077  Z= 1.088
    Chirality :  1.153   5.694    176
    Planarity :  0.017   0.203    326
    Dihedral  : 16.265 120.066    768
    Min Nonbonded Distance : 1.628
  
  Molprobity Statistics.
    All-atom Clashscore : 9.47
    Ramachandran Plot:
      Outliers : 10.95 %
      Allowed  : 11.68 %
      Favored  : 77.37 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  8.87 %
      Favored  : 86.29 %
    Cbeta Deviations :  9.85 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 12.98 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.79 (0.70), residues: 137
    helix: -1.64 (0.55), residues: 61
    sheet:  None (None), residues: 0
    loop : -3.42 (0.79), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A  43 
   PHE   0.167   0.034   PHE A  67 
   TYR   0.457   0.038   TYR A  91 
   ARG   0.035   0.007   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A  43 
   PHE   0.091   0.033   PHE A  67 
   TYR   0.365   0.044   TYR A  91 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =  10.95 %
                favored =  77.37 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =    13
  Clashscore            =   9.47
  RMS(bonds)            =   0.0112
  RMS(angles)           =   2.44
  MolProbity score      =   2.79

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.037 (Z=  2.936)
  Mean delta:    0.013 (Z=  0.668)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 112  VAL  CG1
   A 112  VAL  CB
   A 112  VAL  CG2       110.80    99.48    11.32  2.20e+00  2.65e+01   5.1*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.81     4.79  1.00e+00  2.29e+01   4.8*sigma
   A 112  VAL  CA
   A 112  VAL  CB
   A 112  VAL  CG1       110.40   118.05    -7.65  1.70e+00  2.03e+01   4.5*sigma
   A 139  HIS  CA
   A 139  HIS  CB
   A 139  HIS  CG        113.80   118.08    -4.28  1.00e+00  1.83e+01   4.3*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.79     5.41  1.30e+00  1.73e+01   4.2*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   116.72    -4.12  1.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   11.321 (Z=  5.146)
  Mean delta:    1.851 (Z=  1.025)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   157.64    22.36  5.00e+00  2.00e+01   4.5*sigma

  Min. delta:    0.004
  Max. delta:   87.817
  Mean delta:   18.666

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.308
  Mean delta:    0.090

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.091       0.160      165.39   8.0*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  ND1
   A 139  HIS  CD2
   A 139  HIS  CE1
   A 139  HIS  NE2           0.073       0.113       80.84   5.7*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.092       0.108      167.89   5.4*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.051       0.096       51.42   4.8*sigma

  Min. delta:    0.000
  Max. delta:    0.115
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.476
    Angle     :  1.718  11.321   4079  Z= 0.762
    Chirality :  0.090   0.308    176
    Planarity :  0.015   0.104    327
    Dihedral  : 15.205  87.817    769
    Min Nonbonded Distance : 1.744
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  6.57 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  9.68 %
      Favored  : 86.29 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.40 (0.71), residues: 137
    helix:  0.25 (0.60), residues: 61
    sheet:  None (None), residues: 0
    loop : -0.64 (0.77), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.005   HIS A 136 
   PHE   0.089   0.025   PHE A  45 
   TYR   0.211   0.042   TYR A  91 
   ARG   0.095   0.012   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.005   HIS A 136 
   PHE   0.051   0.022   PHE A  45 
   TYR   0.160   0.040   TYR A  50 
   ARG   0.003   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  93.43 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     1
  Clashscore            =   2.71
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.72
  MolProbity score      =   1.95

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.57    -0.12  1.60e-02  5.57e+01   7.5*sigma
   A  77  ILE  N
   A  77  ILE  CA          1.46     1.55    -0.10  1.90e-02  2.56e+01   5.1*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.63    -0.10  2.10e-02  2.28e+01   4.8*sigma
   A  89  TYR  N
   A  89  TYR  CA          1.46     1.55    -0.09  1.90e-02  2.19e+01   4.7*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.119 (Z=  7.461)
  Mean delta:    0.016 (Z=  0.842)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   144.83   -23.13  1.80e+00  1.65e+02  12.9*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   126.03   -15.53  1.70e+00  8.35e+01   9.1*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   137.20   -15.50  1.80e+00  7.41e+01   8.6*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   125.25   -15.15  1.90e+00  6.35e+01   8.0*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   126.76   -15.16  2.00e+00  5.75e+01   7.6*sigma
   A  76  SER  C
   A  76  SER  CA
   A  76  SER  CB        110.10   124.33   -14.23  1.90e+00  5.61e+01   7.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.09   -11.19  1.50e+00  5.57e+01   7.5*sigma
   A 137  HIS  CA
   A 137  HIS  CB
   A 137  HIS  CG        113.80   121.06    -7.26  1.00e+00  5.27e+01   7.3*sigma
   A  76  SER  N
   A  76  SER  CA
   A  76  SER  CB        110.50    98.42    12.08  1.70e+00  5.05e+01   7.1*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   119.30    -6.70  1.00e+00  4.49e+01   6.7*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    92.43    18.57  2.80e+00  4.40e+01   6.6*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.49    -5.89  1.00e+00  3.47e+01   5.9*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.30   -10.60  1.80e+00  3.47e+01   5.9*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N         116.20   127.80   -11.60  2.00e+00  3.37e+01   5.8*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   120.16    -9.66  1.70e+00  3.23e+01   5.7*sigma
   A  88  ASP  O
   A  88  ASP  C
   A  89  TYR  N         123.00   114.15     8.85  1.60e+00  3.06e+01   5.5*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   131.45    -9.75  1.80e+00  2.93e+01   5.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.08    -9.38  1.80e+00  2.72e+01   5.2*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   113.03     8.67  1.80e+00  2.32e+01   4.8*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   118.56    -4.76  1.00e+00  2.27e+01   4.8*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50   103.45     8.05  1.70e+00  2.24e+01   4.7*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   130.05    -8.35  1.80e+00  2.15e+01   4.6*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   118.34    -7.84  1.70e+00  2.13e+01   4.6*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   120.77    -9.17  2.00e+00  2.10e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.05     4.55  1.00e+00  2.07e+01   4.6*sigma
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        121.70   129.85    -8.15  1.80e+00  2.05e+01   4.5*sigma
   A  76  SER  CA
   A  76  SER  C
   A  76  SER  O         120.80   113.14     7.66  1.70e+00  2.03e+01   4.5*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   107.55     8.65  2.00e+00  1.87e+01   4.3*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   121.65    -7.75  1.80e+00  1.85e+01   4.3*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.68     5.52  1.30e+00  1.80e+01   4.2*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   118.12    -8.02  1.90e+00  1.78e+01   4.2*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10    99.90     9.20  2.20e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   129.02    -7.32  1.80e+00  1.65e+01   4.1*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   124.32    -8.12  2.00e+00  1.65e+01   4.1*sigma
   A  95  ASP  N
   A  95  ASP  CA
   A  95  ASP  CB        110.50   117.39    -6.89  1.70e+00  1.64e+01   4.1*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   128.99    -7.29  1.80e+00  1.64e+01   4.1*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  CB        110.50   117.30    -6.80  1.70e+00  1.60e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   23.132 (Z= 12.851)
  Mean delta:    2.733 (Z=  1.487)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    86.15    93.85  5.00e+00  3.52e+02  18.8*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00    97.30    82.70  5.00e+00  2.74e+02  16.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -98.86   -81.14  5.00e+00  2.63e+02  16.2*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   116.01    63.99  5.00e+00  1.64e+02  12.8*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   125.82    54.18  5.00e+00  1.17e+02  10.8*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   130.48    49.52  5.00e+00  9.81e+01   9.9*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -140.72   -39.28  5.00e+00  6.17e+01   7.9*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   141.77    38.23  5.00e+00  5.84e+01   7.6*sigma
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00  -143.97   -36.03  5.00e+00  5.19e+01   7.2*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00  -146.53   -33.47  5.00e+00  4.48e+01   6.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA          0.00    32.70   -32.70  5.00e+00  4.28e+01   6.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA          0.00   -32.55    32.55  5.00e+00  4.24e+01   6.5*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00  -149.97   -30.03  5.00e+00  3.61e+01   6.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   157.17    22.83  5.00e+00  2.08e+01   4.6*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   158.75    21.25  5.00e+00  1.81e+01   4.2*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00  -158.99   -21.01  5.00e+00  1.77e+01   4.2*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   159.94    20.06  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.086
  Max. delta:   93.848
  Mean delta:   17.039

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.09     5.60  2.00e-01  7.85e+02  28.0*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.67     5.32  2.00e-01  7.07e+02  26.6*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.72     5.24  2.00e-01  6.87e+02  26.2*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.51     5.02  2.00e-01  6.29e+02  25.1*sigma
   A   1  MET  CA
   A   1  MET  N
   A   1  MET  C
   A   1  MET  CB          2.57    -2.25     4.82  2.00e-01  5.81e+02  24.1*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.24     4.75  2.00e-01  5.65e+02  23.8*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.09     4.64  2.00e-01  5.39e+02  23.2*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -1.97     4.48  2.00e-01  5.02e+02  22.4*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.90     4.34  2.00e-01  4.70e+02  21.7*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.08     3.52  2.00e-01  3.09e+02  17.6*sigma

  Min. delta:    0.002
  Max. delta:    5.604
  Mean delta:    1.155

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  ND1
   A 137  HIS  CD2
   A 137  HIS  CE1
   A 137  HIS  NE2           0.081       0.109       99.02   5.5*sigma

  Min. delta:    0.000
  Max. delta:    0.081
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  79  LYS  H  , Angle C-N-H, observed: 111.904, delta from target: 12.396
   A  82  THR  HA , Angle N-CA-HA, observed: 97.126, delta from target: 12.874
   A  92  THR  HB , Angle OG1-CB-HB, observed: 122.015, delta from target: -13.015
   A  51  ILE  HA , Angle CB-CA-HA, observed: 95.350, delta from target: 13.650
   A  76  SER  HA , Angle N-CA-HA, observed: 124.213, delta from target: -14.213
   A  78  ILE  HA , Angle CB-CA-HA, observed: 93.580, delta from target: 15.420
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.968, delta from target: 16.032
   A  79  LYS  HA , Angle C-CA-HA, observed: 125.071, delta from target: -16.071
   A  88  ASP  HA , Angle N-CA-HA, observed: 91.032, delta from target: 18.968
   A  90  SER  HA , Angle N-CA-HA, observed: 90.385, delta from target: 19.615

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.119   2242  Z= 0.599
    Angle     :  2.408  23.132   4079  Z= 1.080
    Chirality :  1.155   5.604    176
    Planarity :  0.013   0.080    327
    Dihedral  : 14.332  93.848    769
    Min Nonbonded Distance : 1.301
  
  Molprobity Statistics.
    All-atom Clashscore : 13.07
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  : 13.14 %
      Favored  : 81.02 %
    Rotamer:
      Outliers :  8.87 %
      Allowed  :  5.65 %
      Favored  : 85.48 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 9.16 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.36 (0.58), residues: 137
    helix: -2.50 (0.45), residues: 72
    sheet:  None (None), residues: 0
    loop : -3.38 (0.70), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 137 
   PHE   0.078   0.015   PHE A  15 
   TYR   0.172   0.028   TYR A  50 
   ARG   0.047   0.007   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 137 
   PHE   0.053   0.013   PHE A  15 
   TYR   0.143   0.031   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   5.84 %
                favored =  81.02 %
  Rotamer outliers      =   8.87 %
  C-beta deviations     =    14
  Clashscore            =  13.07
  RMS(bonds)            =   0.0114
  RMS(angles)           =   2.41
  MolProbity score      =   3.07

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.689)
  Mean delta:    0.012 (Z=  0.643)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.25     4.35  1.00e+00  1.89e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.54     4.06  1.00e+00  1.65e+01   4.1*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.55     4.05  1.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.509 (Z=  4.349)
  Mean delta:    1.801 (Z=  0.983)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   152.37    27.63  5.00e+00  3.05e+01   5.5*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00  -154.97   -25.03  5.00e+00  2.51e+01   5.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA          0.00    24.79   -24.79  5.00e+00  2.46e+01   5.0*sigma
   A 110  ASP  CA
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        180.00   156.29    23.71  5.00e+00  2.25e+01   4.7*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   158.11    21.89  5.00e+00  1.92e+01   4.4*sigma

  Min. delta:    0.022
  Max. delta:   80.263
  Mean delta:   18.303

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.283
  Mean delta:    0.091

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.119       0.117      285.33   5.8*sigma

  Min. delta:    0.000
  Max. delta:    0.119
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.458
    Angle     :  1.675   8.509   4079  Z= 0.735
    Chirality :  0.091   0.283    176
    Planarity :  0.014   0.116    327
    Dihedral  : 15.330  81.961    769
    Min Nonbonded Distance : 1.751
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  : 10.22 %
      Favored  : 87.59 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  3.23 %
      Favored  : 90.32 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.35 (0.60), residues: 137
    helix: -1.14 (0.44), residues: 63
    sheet:  None (None), residues: 0
    loop : -1.96 (0.71), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.031   0.008   HIS A 139 
   PHE   0.128   0.031   PHE A  15 
   TYR   0.267   0.033   TYR A  89 
   ARG   0.056   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.031   0.008   HIS A 139 
   PHE   0.085   0.033   PHE A  15 
   TYR   0.214   0.038   TYR A  89 
   ARG   0.006   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Ramachandran outliers =   2.19 %
                favored =  87.59 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =     0
  Clashscore            =   3.16
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.68
  MolProbity score      =   2.33

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   5"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   4"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.037 (Z=  2.630)
  Mean delta:    0.013 (Z=  0.663)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   115.05     7.55  1.00e+00  5.71e+01   7.6*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   106.46     6.14  1.00e+00  3.77e+01   6.1*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   107.13     5.47  1.00e+00  2.99e+01   5.5*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.18     4.42  1.00e+00  1.96e+01   4.4*sigma
   A 101  LYS  CA
   A 101  LYS  C
   A 102  PRO  N         116.90   122.99    -6.09  1.50e+00  1.65e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    8.181 (Z=  7.553)
  Mean delta:    1.954 (Z=  1.088)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   148.84    31.16  5.00e+00  3.88e+01   6.2*sigma
   A 101  LYS  CA
   A 101  LYS  C
   A 102  PRO  N
   A 102  PRO  CA        180.00   152.15    27.85  5.00e+00  3.10e+01   5.6*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   154.21    25.79  5.00e+00  2.66e+01   5.2*sigma

  Min. delta:    0.155
  Max. delta:   65.411
  Mean delta:   16.228

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.668
  Mean delta:    0.109

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.173       0.316      596.72  15.8*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.161       0.304      518.08  15.2*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.078       0.146      121.17   7.3*sigma
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.076       0.117      101.49   5.9*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.047       0.086       44.14   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.173
  Mean delta:    0.025

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.472
    Angle     :  1.758   8.823   4079  Z= 0.794
    Chirality :  0.109   0.668    176
    Planarity :  0.019   0.158    327
    Dihedral  : 14.797  87.474    769
    Min Nonbonded Distance : 1.591
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  : 13.14 %
      Favored  : 85.40 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  5.65 %
      Favored  : 88.71 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.31 (0.67), residues: 137
    helix: -1.19 (0.48), residues: 68
    sheet:  None (None), residues: 0
    loop : -1.86 (0.83), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.005   HIS A 134 
   PHE   0.188   0.028   PHE A  15 
   TYR   0.376   0.055   TYR A  91 
   ARG   0.079   0.017   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.005   HIS A 134 
   PHE   0.117   0.028   PHE A  15 
   TYR   0.316   0.064   TYR A  91 
   ARG   0.009   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  85.40 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     1
  Clashscore            =   6.76
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.76
  MolProbity score      =   2.60

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.059 (Z=  3.067)
  Mean delta:    0.014 (Z=  0.725)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  98  SER  C
   A  98  SER  CA
   A  98  SER  CB        110.10   132.94   -22.84  1.90e+00  1.44e+02  12.0*sigma
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        121.70   137.06   -15.36  1.80e+00  7.28e+01   8.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.89   -10.99  1.50e+00  5.37e+01   7.3*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   121.56   -11.06  1.70e+00  4.23e+01   6.5*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   133.41   -11.71  1.80e+00  4.23e+01   6.5*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   100.75    10.75  1.70e+00  4.00e+01   6.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   133.08   -11.38  1.80e+00  4.00e+01   6.3*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N         116.20   128.80   -12.60  2.00e+00  3.97e+01   6.3*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   131.58    -9.88  1.80e+00  3.01e+01   5.5*sigma
   A 138  HIS  O
   A 138  HIS  C
   A 139  HIS  N         123.00   114.71     8.29  1.60e+00  2.68e+01   5.2*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.72   -10.12  2.00e+00  2.56e+01   5.1*sigma
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        121.70   130.39    -8.69  1.80e+00  2.33e+01   4.8*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   118.41    -7.91  1.70e+00  2.16e+01   4.7*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10   118.89    -8.79  1.90e+00  2.14e+01   4.6*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   129.98    -8.28  1.80e+00  2.12e+01   4.6*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.13    -4.53  1.00e+00  2.05e+01   4.5*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   123.43   -12.43  2.80e+00  1.97e+01   4.4*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   107.42     8.78  2.00e+00  1.93e+01   4.4*sigma
   A 117  PRO  N
   A 117  PRO  CA
   A 117  PRO  CB        103.00   107.61    -4.61  1.10e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.71e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.53     4.07  1.00e+00  1.65e+01   4.1*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.97     5.23  1.30e+00  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   22.839 (Z= 12.020)
  Mean delta:    2.393 (Z=  1.298)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   -98.65   -81.35  5.00e+00  2.65e+02  16.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   115.48    64.52  5.00e+00  1.67e+02  12.9*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   128.72    51.28  5.00e+00  1.05e+02  10.3*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -142.23   -37.77  5.00e+00  5.71e+01   7.6*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   148.31    31.69  5.00e+00  4.02e+01   6.3*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   151.35    28.65  5.00e+00  3.28e+01   5.7*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   156.18    23.82  5.00e+00  2.27e+01   4.8*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -156.21   -23.79  5.00e+00  2.26e+01   4.8*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   157.65    22.35  5.00e+00  2.00e+01   4.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA          0.00    21.80   -21.80  5.00e+00  1.90e+01   4.4*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   158.74    21.26  5.00e+00  1.81e+01   4.3*sigma

  Min. delta:    0.020
  Max. delta:   87.327
  Mean delta:   15.936

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.71     5.24  2.00e-01  6.86e+02  26.2*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -1.48     3.99  2.00e-01  3.99e+02  20.0*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.10     3.53  2.00e-01  3.11e+02  17.6*sigma

  Min. delta:    0.000
  Max. delta:    5.239
  Mean delta:    0.580

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.072
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  78  ILE  HA , Angle N-CA-HA, observed: 95.261, delta from target: 14.739
   A  51  ILE  HA , Angle CB-CA-HA, observed: 93.574, delta from target: 15.426
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.821, delta from target: 16.179
   A  93  LEU  HA , Angle N-CA-HA, observed: 93.681, delta from target: 16.319
   A  98  SER  HA , Angle N-CA-HA, observed: 127.019, delta from target: -17.019
   A  98  SER  HA , Angle CB-CA-HA, observed: 89.993, delta from target: 19.007
   A  98  SER  HA , Angle C-CA-HA, observed: 88.646, delta from target: 20.354

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.059   2242  Z= 0.516
    Angle     :  2.180  22.839   4079  Z= 0.961
    Chirality :  0.580   5.239    176
    Planarity :  0.010   0.072    327
    Dihedral  : 13.212  87.327    769
    Min Nonbonded Distance : 1.606
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  8.03 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  1.61 %
      Favored  : 93.55 %
    Cbeta Deviations :  6.82 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 3.82 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.14 (0.62), residues: 137
    helix: -1.68 (0.50), residues: 83
    sheet:  None (None), residues: 0
    loop : -2.59 (0.76), residues: 54
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.110   0.017   PHE A  67 
   TYR   0.124   0.019   TYR A 111 
   ARG   0.018   0.003   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.074   0.018   PHE A  67 
   TYR   0.102   0.022   TYR A 111 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   3.65 %
                favored =  88.32 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     9
  Clashscore            =   8.12
  RMS(bonds)            =   0.0099
  RMS(angles)           =   2.18
  MolProbity score      =   2.55

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.555)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.599 (Z=  1.362)
  Mean delta:    0.375 (Z=  0.206)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   88.652
  Mean delta:   23.264

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.097
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.046
    Angle     :  0.980   4.857   4077  Z= 0.342
    Chirality :  0.035   0.097    176
    Planarity :  0.000   0.001    326
    Dihedral  : 17.886  88.652    768
    Min Nonbonded Distance : 1.638
  
  Molprobity Statistics.
    All-atom Clashscore : 19.40
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  : 19.71 %
      Favored  : 75.91 %
    Rotamer:
      Outliers : 18.55 %
      Allowed  : 21.77 %
      Favored  : 59.68 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -7.04 (0.42), residues: 137
    helix: -3.95 (0.39), residues: 68
    sheet:  None (None), residues: 0
    loop : -5.67 (0.42), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.003   0.001   TYR A 105 
   ARG   0.001   0.000   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   TYR A 105 
   ARG   0.000   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  3.000)
  Mean delta:    0.013 (Z=  0.688)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   120.67    -8.07  1.00e+00  6.51e+01   8.1*sigma
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   119.07    -6.47  1.00e+00  4.18e+01   6.5*sigma
   A 102  PRO  C
   A 103  ASP  N
   A 103  ASP  CA        121.70   133.18   -11.48  1.80e+00  4.07e+01   6.4*sigma
   A 102  PRO  CA
   A 102  PRO  N
   A 102  PRO  CD        112.00   105.54     6.46  1.40e+00  2.13e+01   4.6*sigma
   A 103  ASP  C
   A 104  VAL  N
   A 104  VAL  CA        121.70   129.82    -8.12  1.80e+00  2.04e+01   4.5*sigma
   A  44  ASP  C
   A  44  ASP  CA
   A  44  ASP  CB        110.10   118.57    -8.47  1.90e+00  1.99e+01   4.5*sigma
   A 102  PRO  CA
   A 102  PRO  C
   A 103  ASP  N         116.20   107.33     8.87  2.00e+00  1.97e+01   4.4*sigma
   A 102  PRO  N
   A 102  PRO  CA
   A 102  PRO  CB        103.00   107.68    -4.68  1.10e+00  1.81e+01   4.3*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  CD2       131.20   125.71     5.49  1.30e+00  1.78e+01   4.2*sigma
   A  76  SER  C
   A  76  SER  CA
   A  76  SER  CB        110.10   118.01    -7.91  1.90e+00  1.73e+01   4.2*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   129.16    -7.46  1.80e+00  1.72e+01   4.1*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   121.36    -7.46  1.80e+00  1.72e+01   4.1*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.54     4.06  1.00e+00  1.65e+01   4.1*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   117.73    -7.63  1.90e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   11.484 (Z=  8.069)
  Mean delta:    2.138 (Z=  1.181)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   122.89    57.11  5.00e+00  1.30e+02  11.4*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   155.05    24.95  5.00e+00  2.49e+01   5.0*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -155.97   -24.03  5.00e+00  2.31e+01   4.8*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -156.51   -23.49  5.00e+00  2.21e+01   4.7*sigma
   A 100  GLN  CA
   A 100  GLN  C
   A 101  LYS  N
   A 101  LYS  CA        180.00  -156.94   -23.06  5.00e+00  2.13e+01   4.6*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -158.80   -21.20  5.00e+00  1.80e+01   4.2*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   159.20    20.80  5.00e+00  1.73e+01   4.2*sigma

  Min. delta:    0.002
  Max. delta:   85.283
  Mean delta:   18.337

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51    -1.74     4.25  2.00e-01  4.51e+02  21.2*sigma
   A  76  SER  CA
   A  76  SER  N
   A  76  SER  C
   A  76  SER  CB          2.51    -1.63     4.14  2.00e-01  4.29e+02  20.7*sigma
   A 103  ASP  CA
   A 103  ASP  N
   A 103  ASP  C
   A 103  ASP  CB          2.51    -1.51     4.02  2.00e-01  4.05e+02  20.1*sigma

  Min. delta:    0.001
  Max. delta:    4.248
  Mean delta:    0.550

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.054       0.095       58.93   4.8*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.046       0.088       41.93   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.128
  Mean delta:    0.020

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  91  TYR  HA , Angle C-CA-HA, observed: 94.058, delta from target: 14.942
   A 103  ASP  HA , Angle C-CA-HA, observed: 93.333, delta from target: 15.667

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2242  Z= 0.490
    Angle     :  1.932  15.667   4079  Z= 0.866
    Chirality :  0.550   4.248    176
    Planarity :  0.014   0.097    327
    Dihedral  : 15.080  85.283    769
    Min Nonbonded Distance : 1.527
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  6.57 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  4.84 %
      Favored  : 90.32 %
    Cbeta Deviations :  3.03 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.63 (0.70), residues: 137
    helix: -0.87 (0.55), residues: 70
    sheet:  None (None), residues: 0
    loop : -1.22 (0.84), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.021   0.008   HIS A 138 
   PHE   0.045   0.011   PHE A  45 
   TYR   0.114   0.027   TYR A  50 
   ARG   0.104   0.022   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.021   0.008   HIS A 138 
   PHE   0.031   0.008   PHE A  45 
   TYR   0.095   0.028   TYR A  50 
   ARG   0.017   0.003   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   4.38 %
                favored =  75.91 %
  Rotamer outliers      =  18.55 %
  C-beta deviations     =     0
  Clashscore            =  19.40
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.53

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 129}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2216
     H or D atoms   : 1104
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.59    -0.13  1.90e-02  4.94e+01   7.0*sigma
   A  93  LEU  N
   A  93  LEU  CA          1.46     1.36     0.10  1.90e-02  2.87e+01   5.4*sigma
   A  91  TYR  N
   A  91  TYR  CA          1.46     1.54    -0.08  1.90e-02  1.77e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.134 (Z=  7.031)
  Mean delta:    0.016 (Z=  0.825)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   143.58   -21.88  1.80e+00  1.48e+02  12.2*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   132.85   -22.75  1.90e+00  1.43e+02  12.0*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   140.98   -19.28  1.80e+00  1.15e+02  10.7*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   140.94   -19.24  1.80e+00  1.14e+02  10.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20    95.98    20.22  2.00e+00  1.02e+02  10.1*sigma
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        121.70   139.40   -17.70  1.80e+00  9.67e+01   9.8*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   125.80   -15.30  1.70e+00  8.10e+01   9.0*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50    95.67    14.83  1.70e+00  7.61e+01   8.7*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   137.00   -15.30  1.80e+00  7.22e+01   8.5*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   124.78   -14.68  1.90e+00  5.97e+01   7.7*sigma
   A  82  THR  N
   A  82  THR  CA
   A  82  THR  CB        111.50   123.53   -12.03  1.70e+00  5.01e+01   7.1*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   122.23   -11.83  1.70e+00  4.84e+01   7.0*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   109.94    11.76  1.80e+00  4.27e+01   6.5*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O         120.80   131.74   -10.94  1.70e+00  4.14e+01   6.4*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N         116.20   129.07   -12.87  2.00e+00  4.14e+01   6.4*sigma
   A  76  SER  C
   A  76  SER  CA
   A  76  SER  CB        110.10   121.81   -11.71  1.90e+00  3.80e+01   6.2*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   123.67   -12.07  2.00e+00  3.64e+01   6.0*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   132.31   -10.61  1.80e+00  3.48e+01   5.9*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   132.16   -10.46  1.80e+00  3.38e+01   5.8*sigma
   A  92  THR  O
   A  92  THR  C
   A  93  LEU  N         123.00   132.17    -9.17  1.60e+00  3.28e+01   5.7*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.98   -10.28  1.80e+00  3.26e+01   5.7*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   124.65   -10.55  2.00e+00  2.78e+01   5.3*sigma
   A  98  SER  C
   A  98  SER  CA
   A  98  SER  CB        110.10   120.12   -10.02  1.90e+00  2.78e+01   5.3*sigma
   A 138  HIS  O
   A 138  HIS  C
   A 139  HIS  N         123.00   114.78     8.22  1.60e+00  2.64e+01   5.1*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.53    -4.93  1.00e+00  2.43e+01   4.9*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   103.40     8.10  1.70e+00  2.27e+01   4.8*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   125.10    -8.90  2.00e+00  1.98e+01   4.4*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   117.67    -7.17  1.70e+00  1.78e+01   4.2*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   118.10    -8.00  1.90e+00  1.77e+01   4.2*sigma
   A  51  ILE  N
   A  51  ILE  CA
   A  51  ILE  C         111.00   122.78   -11.78  2.80e+00  1.77e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.18    -5.78  1.40e+00  1.70e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma
   A  95  ASP  N
   A  95  ASP  CA
   A  95  ASP  CB        110.50   117.43    -6.93  1.70e+00  1.66e+01   4.1*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   129.03    -7.33  1.80e+00  1.66e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   22.749 (Z= 12.153)
  Mean delta:    2.936 (Z=  1.577)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00    79.12   100.88  5.00e+00  4.07e+02  20.2*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -104.61   -75.39  5.00e+00  2.27e+02  15.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -135.32   -44.68  5.00e+00  7.99e+01   8.9*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -137.95   -42.05  5.00e+00  7.07e+01   8.4*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -139.13   -40.87  5.00e+00  6.68e+01   8.2*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   143.85    36.15  5.00e+00  5.23e+01   7.2*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   144.56    35.44  5.00e+00  5.03e+01   7.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -146.25   -33.75  5.00e+00  4.56e+01   6.8*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   147.60    32.40  5.00e+00  4.20e+01   6.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -150.35   -29.65  5.00e+00  3.52e+01   5.9*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   151.33    28.67  5.00e+00  3.29e+01   5.7*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00  -151.63   -28.37  5.00e+00  3.22e+01   5.7*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   152.49    27.51  5.00e+00  3.03e+01   5.5*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   152.71    27.29  5.00e+00  2.98e+01   5.5*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00  -156.02   -23.98  5.00e+00  2.30e+01   4.8*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   157.09    22.91  5.00e+00  2.10e+01   4.6*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00  -157.29   -22.71  5.00e+00  2.06e+01   4.5*sigma

  Min. delta:    0.006
  Max. delta:  100.882
  Mean delta:   17.273

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -3.04     5.69  2.00e-01  8.09e+02  28.4*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.16     5.67  2.00e-01  8.03e+02  28.3*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.64     5.15  2.00e-01  6.62e+02  25.7*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.76     4.19  2.00e-01  4.39e+02  20.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.20     3.63  2.00e-01  3.30e+02  18.2*sigma
   A  82  THR  CA
   A  82  THR  N
   A  82  THR  C
   A  82  THR  CB          2.53     1.20     1.33  2.00e-01  4.42e+01   6.6*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51     1.36     1.15  2.00e-01  3.31e+01   5.8*sigma
   A  95  ASP  CA
   A  95  ASP  N
   A  95  ASP  C
   A  95  ASP  CB          2.51     1.64     0.87  2.00e-01  1.88e+01   4.3*sigma

  Min. delta:    0.001
  Max. delta:    5.689
  Mean delta:    0.858

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.065       0.122       84.64   6.1*sigma
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CD            0.144       0.249       33.17   5.0*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.052       0.094       54.17   4.7*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.044       0.085       37.93   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.144
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1104
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1104
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="GLY A  80  conformer  : H 
    0" pdbres="LEU A  93  conformer  : H 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  78  ILE  HA , Angle C-CA-HA, observed: 96.754, delta from target: 12.246
   A  92  THR  HB , Angle CA-CB-HB, observed: 96.667, delta from target: 12.333
   A  78  ILE  HA , Angle CB-CA-HA, observed: 96.154, delta from target: 12.846
   A  74  ASP  HA , Angle CB-CA-HA, observed: 95.664, delta from target: 13.336
   A  92  THR  HB , Angle OG1-CB-HB, observed: 122.391, delta from target: -13.391
   A  77  ILE  HB , Angle CA-CB-HB, observed: 95.383, delta from target: 13.617
   A  90  SER  HA , Angle N-CA-HA, observed: 94.810, delta from target: 15.190
   A  95  ASP  HA , Angle N-CA-HA, observed: 94.501, delta from target: 15.499
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.487, delta from target: 15.513
   A  93  LEU  HA , Angle C-CA-HA, observed: 92.539, delta from target: 16.461
   A  51  ILE  HA , Angle N-CA-HA, observed: 92.232, delta from target: 17.768
   A  93  LEU  HA , Angle N-CA-HA, observed: 131.454, delta from target: -21.454
   A  82  THR  HA , Angle N-CA-HA, observed: 83.621, delta from target: 26.379

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.134   2240  Z= 0.588
    Angle     :  2.564  26.379   4075  Z= 1.144
    Chirality :  0.858   5.689    176
    Planarity :  0.014   0.144    325
    Dihedral  : 14.270 100.882    768
    Min Nonbonded Distance : 1.543
  
  Molprobity Statistics.
    All-atom Clashscore : 9.48
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  :  6.57 %
      Favored  : 86.86 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  5.65 %
      Favored  : 87.10 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 6.11 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.50 (0.61), residues: 137
    helix: -1.53 (0.49), residues: 70
    sheet:  None (None), residues: 0
    loop : -3.29 (0.70), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.004   HIS A 138 
   PHE   0.027   0.007   PHE A  67 
   TYR   0.150   0.020   TYR A 111 
   ARG   0.065   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.004   HIS A 138 
   PHE   0.020   0.007   PHE A  67 
   TYR   0.122   0.023   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  91.97 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     4
  Clashscore            =   4.96
  RMS(bonds)            =   0.0094
  RMS(angles)           =   1.93
  MolProbity score      =   2.27

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}
  Ramachandran outliers =   6.57 %
                favored =  86.86 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    14
  Clashscore            =   9.48
  RMS(bonds)            =   0.0112
  RMS(angles)           =   2.56
  MolProbity score      =   2.78

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.643)
  Mean delta:    0.013 (Z=  0.673)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   119.32    -6.72  1.00e+00  4.51e+01   6.7*sigma
   A 127  ARG  NE
   A 127  ARG  CZ
   A 127  ARG  NH2       119.20   124.29    -5.09  9.00e-01  3.20e+01   5.7*sigma
   A 101  LYS  CA
   A 101  LYS  C
   A 102  PRO  N         116.90   123.91    -7.01  1.50e+00  2.19e+01   4.7*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.19     4.41  1.00e+00  1.95e+01   4.4*sigma
   A 127  ARG  NH1
   A 127  ARG  CZ
   A 127  ARG  NH2       119.30   113.67     5.63  1.30e+00  1.88e+01   4.3*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    8.721 (Z=  6.715)
  Mean delta:    1.959 (Z=  1.098)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 101  LYS  CA
   A 101  LYS  C
   A 102  PRO  N
   A 102  PRO  CA        180.00  -150.81   -29.19  5.00e+00  3.41e+01   5.8*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -154.65   -25.35  5.00e+00  2.57e+01   5.1*sigma
   A   1  MET  CA
   A   1  MET  C
   A   2  LEU  N
   A   2  LEU  CA        180.00  -159.14   -20.86  5.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.006
  Max. delta:   70.913
  Mean delta:   15.825

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.407
  Mean delta:    0.099

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  67  PHE  CB
   A  67  PHE  CG
   A  67  PHE  CD1
   A  67  PHE  CD2
   A  67  PHE  CE1
   A  67  PHE  CE2
   A  67  PHE  CZ            0.115       0.133      230.39   6.7*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.125       0.107      314.10   5.3*sigma

  Min. delta:    0.000
  Max. delta:    0.125
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.479
    Angle     :  1.782  10.059   4079  Z= 0.804
    Chirality :  0.099   0.407    176
    Planarity :  0.014   0.120    327
    Dihedral  : 13.646  70.913    769
    Min Nonbonded Distance : 1.722
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  8.76 %
      Favored  : 87.59 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.38 (0.66), residues: 137
    helix: -0.68 (0.52), residues: 67
    sheet:  None (None), residues: 0
    loop : -2.57 (0.76), residues: 70
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 137 
   PHE   0.283   0.044   PHE A  67 
   TYR   0.286   0.031   TYR A  81 
   ARG   0.035   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 137 
   PHE   0.187   0.045   PHE A  67 
   TYR   0.232   0.033   TYR A  81 
   ARG   0.009   0.003   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.032 (Z=  1.519)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.606 (Z=  1.358)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   89.637
  Mean delta:   24.152

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.095
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.032   2241  Z= 0.045
    Angle     :  0.980   4.829   4077  Z= 0.342
    Chirality :  0.035   0.095    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.913  89.637    768
    Min Nonbonded Distance : 1.464
  
  Molprobity Statistics.
    All-atom Clashscore : 18.94
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  : 19.71 %
      Favored  : 75.91 %
    Rotamer:
      Outliers : 21.77 %
      Allowed  : 20.16 %
      Favored  : 58.06 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.36 (0.51), residues: 137
    helix: -3.92 (0.40), residues: 60
    sheet:  None (None), residues: 0
    loop : -4.71 (0.58), residues: 77
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 136 
   PHE   0.001   0.001   PHE A  15 
   TYR   0.002   0.001   TYR A  81 
   ARG   0.001   0.000   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 136 
   PHE   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A  91 
   ARG   0.000   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.894, 58.223, 40.328, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   3.65 %
                favored =  87.59 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.78
  MolProbity score      =   2.37

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (39.622, 57.786, 57.981, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  10"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   4.38 %
                favored =  75.91 %
  Rotamer outliers      =  21.77 %
  C-beta deviations     =     0
  Clashscore            =  18.94
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.58

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.044 (Z=  2.762)
  Mean delta:    0.013 (Z=  0.677)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  43  HIS  CA
   A  43  HIS  CB
   A  43  HIS  CG        113.80   118.63    -4.83  1.00e+00  2.33e+01   4.8*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.79     4.81  1.00e+00  2.32e+01   4.8*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.38     5.82  1.30e+00  2.01e+01   4.5*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.42     5.78  1.30e+00  1.98e+01   4.4*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    9.527 (Z=  4.826)
  Mean delta:    2.009 (Z=  1.102)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00  -140.58   -39.42  5.00e+00  6.22e+01   7.9*sigma
   A  42  GLY  CA
   A  42  GLY  C
   A  43  HIS  N
   A  43  HIS  CA        180.00  -155.84   -24.16  5.00e+00  2.33e+01   4.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   156.51    23.49  5.00e+00  2.21e+01   4.7*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   157.10    22.90  5.00e+00  2.10e+01   4.6*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   158.09    21.91  5.00e+00  1.92e+01   4.4*sigma

  Min. delta:    0.059
  Max. delta:   81.404
  Mean delta:   17.937

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.520
  Mean delta:    0.108

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  ND1
   A 135  HIS  CD2
   A 135  HIS  CE1
   A 135  HIS  NE2           0.052       0.082       41.26   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.063
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   14" pdbres="HIS A  43  conformer  : HE2, HD1 
   14" pdbres="HIS A 134  conformer  : HE2, HD1 
   14" pdbres="HIS A 135  conformer  : HE2, HD1 
   14" pdbres="HIS A 136  conformer  : HE2, HD1 
   14" pdbres="HIS A 137  conformer  : HE2, HD1 
   14" pdbres="HIS A 138  conformer  : HE2, HD1 
   14" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.044   2242  Z= 0.482
    Angle     :  1.823  11.805   4079  Z= 0.812
    Chirality :  0.108   0.520    176
    Planarity :  0.012   0.068    327
    Dihedral  : 14.992  81.404    769
    Min Nonbonded Distance : 1.563
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.11 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  8.06 %
      Favored  : 86.29 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.13 (0.75), residues: 137
    helix: -1.17 (0.54), residues: 64
    sheet:  None (None), residues: 0
    loop : -0.19 (0.89), residues: 73
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.029   0.005   HIS A  43 
   PHE   0.122   0.034   PHE A  15 
   TYR   0.122   0.024   TYR A 111 
   ARG   0.029   0.007   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.029   0.005   HIS A  43 
   PHE   0.081   0.028   PHE A  15 
   TYR   0.096   0.028   TYR A 111 
   ARG   0.002   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.032 (Z=  1.542)
  Mean delta:    0.001 (Z=  0.061)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.598 (Z=  1.325)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   85.242
  Mean delta:   22.929

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.095
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.032   2241  Z= 0.045
    Angle     :  0.979   4.849   4077  Z= 0.341
    Chirality :  0.035   0.095    176
    Planarity :  0.000   0.001    326
    Dihedral  : 17.987  85.242    768
    Min Nonbonded Distance : 1.502
  
  Molprobity Statistics.
    All-atom Clashscore : 19.85
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  : 19.71 %
      Favored  : 79.56 %
    Rotamer:
      Outliers : 21.77 %
      Allowed  : 18.55 %
      Favored  : 59.68 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.70 (0.41), residues: 137
    helix: -4.01 (0.35), residues: 69
    sheet:  None (None), residues: 0
    loop : -5.08 (0.46), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 135 
   PHE   0.003   0.001   PHE A  15 
   TYR   0.003   0.001   TYR A 105 
   ARG   0.001   0.000   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 135 
   PHE   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A 105 
   ARG   0.001   0.000   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A 135  HIS

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Ramachandran outliers =   2.19 %
                favored =  92.70 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.82
  MolProbity score      =   2.47

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  79.56 %
  Rotamer outliers      =  21.77 %
  C-beta deviations     =     0
  Clashscore            =  19.85
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.55

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 128  MET  CA
   A 128  MET  CB          1.53     1.66    -0.13  2.00e-02  4.29e+01   6.6*sigma
   A 128  MET  CA
   A 128  MET  C           1.52     1.41     0.12  2.10e-02  3.14e+01   5.6*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.37     0.08  1.90e-02  1.97e+01   4.4*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.52    -0.07  1.60e-02  1.76e+01   4.2*sigma
   A 123  GLU  N
   A 123  GLU  CA          1.46     1.38     0.08  1.90e-02  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.131 (Z=  6.552)
  Mean delta:    0.017 (Z=  0.892)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   174.44   -57.54  1.50e+00  1.47e+03  38.4*sigma
   A  51  ILE  O
   A  51  ILE  C
   A  52  PRO  N         123.00    87.20    35.80  1.60e+00  5.01e+02  22.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80    87.30    33.50  1.70e+00  3.88e+02  19.7*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG1       110.40   134.14   -23.74  1.70e+00  1.95e+02  14.0*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00   148.47   -37.47  2.80e+00  1.79e+02  13.4*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10    91.12    18.98  1.90e+00  9.98e+01  10.0*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   127.09   -16.59  1.70e+00  9.53e+01   9.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20    97.86    18.34  2.00e+00  8.41e+01   9.2*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   137.97   -16.27  1.80e+00  8.17e+01   9.0*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   134.45   -23.45  2.80e+00  7.02e+01   8.4*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   136.29   -14.59  1.80e+00  6.57e+01   8.1*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   107.36    14.34  1.80e+00  6.34e+01   8.0*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   107.49    14.21  1.80e+00  6.23e+01   7.9*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   121.51    -7.71  1.00e+00  5.95e+01   7.7*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   122.91   -12.41  1.70e+00  5.33e+01   7.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   102.10    14.10  2.00e+00  4.97e+01   7.0*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   122.21   -11.81  1.70e+00  4.83e+01   6.9*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   126.24   -12.34  1.80e+00  4.70e+01   6.9*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50    99.37    11.13  1.70e+00  4.28e+01   6.5*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   110.25    11.45  1.80e+00  4.05e+01   6.4*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   110.38    11.32  1.80e+00  3.96e+01   6.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   131.32   -10.52  1.70e+00  3.83e+01   6.2*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N         116.20   104.14    12.06  2.00e+00  3.63e+01   6.0*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50   121.75   -10.25  1.70e+00  3.63e+01   6.0*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   119.52    -9.02  1.50e+00  3.61e+01   6.0*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10    98.95    11.15  1.90e+00  3.44e+01   5.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.40    -5.80  1.00e+00  3.37e+01   5.8*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   124.17   -10.27  1.80e+00  3.25e+01   5.7*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N         116.20   104.88    11.32  2.00e+00  3.21e+01   5.7*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   120.22   -10.12  1.90e+00  2.84e+01   5.3*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   120.11   -10.01  1.90e+00  2.78e+01   5.3*sigma
   A 138  HIS  N
   A 138  HIS  CA
   A 138  HIS  CB        110.50   119.39    -8.89  1.70e+00  2.74e+01   5.2*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N         116.20   105.92    10.28  2.00e+00  2.64e+01   5.1*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   130.86    -9.16  1.80e+00  2.59e+01   5.1*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   130.83    -9.13  1.80e+00  2.57e+01   5.1*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   125.16   -14.16  2.80e+00  2.56e+01   5.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   102.20     8.30  1.70e+00  2.38e+01   4.9*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   113.05     8.65  1.80e+00  2.31e+01   4.8*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O         120.80   128.93    -8.13  1.70e+00  2.29e+01   4.8*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   113.32     8.38  1.80e+00  2.17e+01   4.7*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   118.41    -7.91  1.70e+00  2.16e+01   4.7*sigma
   A 138  HIS  O
   A 138  HIS  C
   A 139  HIS  N         123.00   115.61     7.39  1.60e+00  2.14e+01   4.6*sigma
   A  48  ALA  N
   A  48  ALA  CA
   A  48  ALA  CB        110.40   117.29    -6.89  1.50e+00  2.11e+01   4.6*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00    98.22    12.78  2.80e+00  2.08e+01   4.6*sigma
   A 126  VAL  O
   A 126  VAL  C
   A 127  ARG  N         123.00   130.24    -7.24  1.60e+00  2.05e+01   4.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.41     5.79  1.30e+00  1.99e+01   4.5*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   113.77     7.93  1.80e+00  1.94e+01   4.4*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   129.57    -7.87  1.80e+00  1.91e+01   4.4*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   109.44     4.36  1.00e+00  1.90e+01   4.4*sigma
   A 128  MET  CA
   A 128  MET  CB
   A 128  MET  CG        114.10   122.70    -8.60  2.00e+00  1.85e+01   4.3*sigma
   A  52  PRO  C
   A  52  PRO  CA
   A  52  PRO  CB        110.10   118.22    -8.12  1.90e+00  1.83e+01   4.3*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N         116.20   107.82     8.38  2.00e+00  1.76e+01   4.2*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  CB        111.50   104.38     7.12  1.70e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.45     4.15  1.00e+00  1.72e+01   4.2*sigma
   A 120  GLU  O
   A 120  GLU  C
   A 121  GLY  N         123.00   129.64    -6.64  1.60e+00  1.72e+01   4.2*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   119.89    -8.29  2.00e+00  1.72e+01   4.1*sigma
   A 117  PRO  N
   A 117  PRO  CA
   A 117  PRO  C         112.10   122.38   -10.28  2.50e+00  1.69e+01   4.1*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.86     5.34  1.30e+00  1.69e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A 122  ILE  C
   A 122  ILE  CA
   A 122  ILE  CB        111.60   103.41     8.19  2.00e+00  1.68e+01   4.1*sigma
   A  48  ALA  C
   A  48  ALA  CA
   A  48  ALA  CB        110.50   116.57    -6.07  1.50e+00  1.64e+01   4.0*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   117.26    -6.86  1.70e+00  1.63e+01   4.0*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   128.96    -7.26  1.80e+00  1.63e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:   57.538 (Z= 38.359)
  Mean delta:    3.840 (Z=  2.128)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   -49.31  -130.69  5.00e+00  6.83e+02  26.1*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00    56.58   123.42  5.00e+00  6.09e+02  24.7*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   -68.18  -111.82  5.00e+00  5.00e+02  22.4*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   -77.37  -102.63  5.00e+00  4.21e+02  20.5*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    87.94    92.06  5.00e+00  3.39e+02  18.4*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   102.77    77.23  5.00e+00  2.39e+02  15.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -110.08   -69.92  5.00e+00  1.96e+02  14.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -110.69   -69.31  5.00e+00  1.92e+02  13.9*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   111.37    68.63  5.00e+00  1.88e+02  13.7*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -114.73   -65.27  5.00e+00  1.70e+02  13.1*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00  -115.05   -64.95  5.00e+00  1.69e+02  13.0*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -121.01   -58.99  5.00e+00  1.39e+02  11.8*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   133.22    46.78  5.00e+00  8.75e+01   9.4*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   133.40    46.60  5.00e+00  8.69e+01   9.3*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -134.95   -45.05  5.00e+00  8.12e+01   9.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA          0.00   -38.96    38.96  5.00e+00  6.07e+01   7.8*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   141.20    38.80  5.00e+00  6.02e+01   7.8*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -142.89   -37.11  5.00e+00  5.51e+01   7.4*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -143.83   -36.17  5.00e+00  5.23e+01   7.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA          0.00    34.45   -34.45  5.00e+00  4.75e+01   6.9*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   147.73    32.27  5.00e+00  4.16e+01   6.5*sigma
   A  48  ALA  CA
   A  48  ALA  C
   A  49  GLU  N
   A  49  GLU  CA        180.00   148.48    31.52  5.00e+00  3.97e+01   6.3*sigma
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00  -155.00   -25.00  5.00e+00  2.50e+01   5.0*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00  -155.75   -24.25  5.00e+00  2.35e+01   4.8*sigma
   A  52  PRO  CA
   A  52  PRO  C
   A  53  LEU  N
   A  53  LEU  CA        180.00  -156.68   -23.32  5.00e+00  2.17e+01   4.7*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   159.31    20.69  5.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.026
  Max. delta:  130.688
  Mean delta:   22.540

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.87     5.38  2.00e-01  7.25e+02  26.9*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.62     5.13  2.00e-01  6.57e+02  25.6*sigma
   A   1  MET  CA
   A   1  MET  N
   A   1  MET  C
   A   1  MET  CB          2.57    -2.41     4.97  2.00e-01  6.19e+02  24.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -2.43     4.87  2.00e-01  5.92e+02  24.3*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.19     4.84  2.00e-01  5.85e+02  24.2*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.30     4.74  2.00e-01  5.62e+02  23.7*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -2.20     4.71  2.00e-01  5.55e+02  23.6*sigma
   A 138  HIS  CA
   A 138  HIS  N
   A 138  HIS  C
   A 138  HIS  CB          2.51    -2.07     4.58  2.00e-01  5.24e+02  22.9*sigma
   A 135  HIS  CA
   A 135  HIS  N
   A 135  HIS  C
   A 135  HIS  CB          2.51    -1.97     4.48  2.00e-01  5.01e+02  22.4*sigma
   A 133  GLU  CA
   A 133  GLU  N
   A 133  GLU  C
   A 133  GLU  CB          2.51    -1.96     4.47  2.00e-01  5.00e+02  22.4*sigma
   A 120  GLU  CA
   A 120  GLU  N
   A 120  GLU  C
   A 120  GLU  CB          2.51    -1.86     4.37  2.00e-01  4.78e+02  21.9*sigma
   A 132  LEU  CA
   A 132  LEU  N
   A 132  LEU  C
   A 132  LEU  CB          2.51    -1.81     4.32  2.00e-01  4.67e+02  21.6*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -1.35     3.86  2.00e-01  3.73e+02  19.3*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43     0.90     1.53  2.00e-01  5.84e+01   7.6*sigma
   A  48  ALA  CA
   A  48  ALA  N
   A  48  ALA  C
   A  48  ALA  CB          2.48     1.48     1.01  2.00e-01  2.53e+01   5.0*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48     1.57     0.91  2.00e-01  2.09e+01   4.6*sigma

  Min. delta:    0.001
  Max. delta:    5.384
  Mean delta:    1.293

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.134       0.240      357.89  12.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 121  GLY  O
   A 122  ILE  N             0.050       0.087       25.33   4.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  89  TYR  O
   A  90  SER  N             0.049       0.085       23.91   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.134
  Mean delta:    0.021

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  78  ILE  HB , Angle CA-CB-HB, observed: 96.810, delta from target: 12.190
   A 120  GLU  HA , Angle C-CA-HA, observed: 96.546, delta from target: 12.454
   A  78  ILE  HA , Angle N-CA-HA, observed: 97.276, delta from target: 12.724
   A  79  LYS  HA , Angle CB-CA-HA, observed: 121.862, delta from target: -12.862
   A 122  ILE  HB , Angle CG1-CB-HB, observed: 95.671, delta from target: 13.329
   A  89  TYR  HA , Angle N-CA-HA, observed: 95.423, delta from target: 14.577
   A 127  ARG  HA , Angle CB-CA-HA, observed: 91.507, delta from target: 17.493
   A  81  TYR  HA , Angle C-CA-HA, observed: 128.109, delta from target: -19.109
   A 122  ILE  HA , Angle N-CA-HA, observed: 90.467, delta from target: 19.533
   A 124  ALA  HA , Angle C-CA-HA, observed: 88.171, delta from target: 20.829
   A 131  ILE  HA , Angle C-CA-HA, observed: 87.735, delta from target: 21.265
   A 122  ILE  HB , Angle CG2-CB-HB, observed: 132.436, delta from target: -23.436
   A  78  ILE  HA , Angle CB-CA-HA, observed: 134.246, delta from target: -25.246
   A 128  MET  HA , Angle N-CA-HA, observed: 76.420, delta from target: 33.580
   A 128  MET  HA , Angle CB-CA-HA, observed: 147.385, delta from target: -38.385
   A  78  ILE  HA , Angle C-CA-HA, observed: 65.158, delta from target: 43.842

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.131   2242  Z= 0.635
    Angle     :  3.218  57.538   4079  Z= 1.497
    Chirality :  1.293   5.384    176
    Planarity :  0.016   0.126    327
    Dihedral  : 18.019 130.688    769
    Min Nonbonded Distance : 1.528
  
  Molprobity Statistics.
    All-atom Clashscore : 24.80
    Ramachandran Plot:
      Outliers : 12.41 %
      Allowed  : 11.68 %
      Favored  : 75.91 %
    Rotamer:
      Outliers : 10.48 %
      Allowed  :  4.03 %
      Favored  : 85.48 %
    Cbeta Deviations : 16.67 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 16.03 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.51 (0.61), residues: 137
    helix: -2.30 (0.48), residues: 65
    sheet:  None (None), residues: 0
    loop : -3.80 (0.71), residues: 72
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.052   0.012   PHE A  45 
   TYR   0.292   0.029   TYR A  50 
   ARG   0.028   0.004   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A  43 
   PHE   0.038   0.013   PHE A  45 
   TYR   0.240   0.033   TYR A  50 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.035 (Z=  2.603)
  Mean delta:    0.013 (Z=  0.662)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   133.01   -11.31  1.80e+00  3.95e+01   6.3*sigma
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        121.70   132.46   -10.76  1.80e+00  3.57e+01   6.0*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   118.78    -4.98  1.00e+00  2.48e+01   5.0*sigma
   A  43  HIS  C
   A  44  ASP  N
   A  44  ASP  CA        121.70   129.92    -8.22  1.80e+00  2.08e+01   4.6*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  CB        110.50   117.62    -7.12  1.70e+00  1.75e+01   4.2*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   11.313 (Z=  6.285)
  Mean delta:    2.115 (Z=  1.145)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -135.30   -44.70  5.00e+00  7.99e+01   8.9*sigma
   A  44  ASP  CA
   A  44  ASP  C
   A  45  PHE  N
   A  45  PHE  CA        180.00  -147.86   -32.14  5.00e+00  4.13e+01   6.4*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   153.66    26.34  5.00e+00  2.78e+01   5.3*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   153.87    26.13  5.00e+00  2.73e+01   5.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -155.84   -24.16  5.00e+00  2.34e+01   4.8*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -159.51   -20.49  5.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.058
  Max. delta:   87.263
  Mean delta:   17.888

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -2.05     4.56  2.00e-01  5.19e+02  22.8*sigma
   A 129  ARG  CA
   A 129  ARG  N
   A 129  ARG  C
   A 129  ARG  CB          2.51    -1.93     4.44  2.00e-01  4.92e+02  22.2*sigma
   A  44  ASP  CA
   A  44  ASP  N
   A  44  ASP  C
   A  44  ASP  CB          2.51    -1.66     4.17  2.00e-01  4.34e+02  20.8*sigma
   A 113  LYS  CA
   A 113  LYS  N
   A 113  LYS  C
   A 113  LYS  CB          2.51    -1.50     4.01  2.00e-01  4.01e+02  20.0*sigma

  Min. delta:    0.001
  Max. delta:    4.556
  Mean delta:    0.658

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.125       0.242      314.22  12.1*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.065       0.095       84.42   4.7*sigma

  Min. delta:    0.000
  Max. delta:    0.125
  Mean delta:    0.021

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   13" pdbres="HIS A  43  conformer  : HE2, HD1 
   13" pdbres="HIS A 134  conformer  : HE2, HD1 
   13" pdbres="HIS A 135  conformer  : HE2, HD1 
   13" pdbres="HIS A 136  conformer  : HE2, HD1 
   13" pdbres="HIS A 137  conformer  : HE2, HD1 
   13" pdbres="HIS A 138  conformer  : HE2, HD1 
   13" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  44  ASP  HA , Angle C-CA-HA, observed: 95.828, delta from target: 13.172
   A 113  LYS  HA , Angle C-CA-HA, observed: 91.767, delta from target: 17.233

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.035   2242  Z= 0.472
    Angle     :  1.923  17.233   4079  Z= 0.847
    Chirality :  0.658   4.556    176
    Planarity :  0.016   0.134    327
    Dihedral  : 14.888  87.263    769
    Min Nonbonded Distance : 1.528
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  3.65 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  5.65 %
      Favored  : 91.13 %
    Cbeta Deviations :  5.30 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 1.53 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.68 (0.65), residues: 137
    helix: -0.24 (0.56), residues: 64
    sheet:  None (None), residues: 0
    loop : -1.98 (0.70), residues: 73
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.006   HIS A 134 
   PHE   0.063   0.017   PHE A  67 
   TYR   0.320   0.042   TYR A  91 
   ARG   0.097   0.020   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.006   HIS A 134 
   PHE   0.043   0.017   PHE A  67 
   TYR   0.242   0.039   TYR A  91 
   ARG   0.007   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =  12.41 %
                favored =  75.91 %
  Rotamer outliers      =  10.48 %
  C-beta deviations     =    22
  Clashscore            =  24.80
  RMS(bonds)            =   0.0123
  RMS(angles)           =   3.22
  MolProbity score      =   3.44

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   9"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   2.19 %
                favored =  94.16 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     7
  Clashscore            =   3.16
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.92
  MolProbity score      =   1.89

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.892)
  Mean delta:    0.013 (Z=  0.666)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.75     4.85  1.00e+00  2.35e+01   4.8*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.734 (Z=  4.847)
  Mean delta:    1.996 (Z=  1.068)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A   2  LEU  CA
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        180.00  -150.03   -29.97  5.00e+00  3.59e+01   6.0*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   150.89    29.11  5.00e+00  3.39e+01   5.8*sigma

  Min. delta:    0.013
  Max. delta:   89.137
  Mean delta:   20.032

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.422
  Mean delta:    0.102

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.058       0.098       66.59   4.9*sigma
   A  68  TYR  CB
   A  68  TYR  CG
   A  68  TYR  CD1
   A  68  TYR  CD2
   A  68  TYR  CE1
   A  68  TYR  CE2
   A  68  TYR  CZ
   A  68  TYR  OH            0.049       0.092       48.69   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.077
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   11" pdbres="HIS A  43  conformer  : HE2, HD1 
   11" pdbres="HIS A 134  conformer  : HE2, HD1 
   11" pdbres="HIS A 135  conformer  : HE2, HD1 
   11" pdbres="HIS A 136  conformer  : HE2, HD1 
   11" pdbres="HIS A 137  conformer  : HE2, HD1 
   11" pdbres="HIS A 138  conformer  : HE2, HD1 
   11" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.474
    Angle     :  1.802   7.964   4079  Z= 0.790
    Chirality :  0.102   0.422    176
    Planarity :  0.012   0.059    327
    Dihedral  : 15.809  89.137    769
    Min Nonbonded Distance : 1.793
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  : 10.22 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  8.87 %
      Favored  : 85.48 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.31 (0.68), residues: 137
    helix: -0.85 (0.59), residues: 61
    sheet:  None (None), residues: 0
    loop : -2.18 (0.73), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A  43 
   PHE   0.043   0.010   PHE A  45 
   TYR   0.123   0.026   TYR A  68 
   ARG   0.066   0.012   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A  43 
   PHE   0.018   0.007   PHE A  45 
   TYR   0.098   0.028   TYR A  12 
   ARG   0.004   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 125  LYS  N
   A 125  LYS  CA          1.46     1.55    -0.10  1.90e-02  2.55e+01   5.0*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     1.55    -0.09  1.90e-02  2.46e+01   5.0*sigma
   A 130  SER  CA
   A 130  SER  C           1.52     1.62    -0.10  2.10e-02  2.05e+01   4.5*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.096 (Z=  5.049)
  Mean delta:    0.016 (Z=  0.825)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG1       110.40   124.80   -14.40  1.70e+00  7.18e+01   8.5*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   106.45    15.25  1.80e+00  7.17e+01   8.5*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   124.87   -14.77  1.90e+00  6.04e+01   7.8*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   108.15    13.55  1.80e+00  5.67e+01   7.5*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   126.15   -14.55  2.00e+00  5.29e+01   7.3*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   121.33   -10.83  1.50e+00  5.21e+01   7.2*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   134.51   -12.81  1.80e+00  5.07e+01   7.1*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40    99.81    10.59  1.50e+00  4.98e+01   7.1*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   122.41   -11.91  1.70e+00  4.91e+01   7.0*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   133.97   -12.27  1.80e+00  4.64e+01   6.8*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   109.66    12.04  1.80e+00  4.47e+01   6.7*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00   129.47   -18.47  2.80e+00  4.35e+01   6.6*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   109.84    11.86  1.80e+00  4.34e+01   6.6*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10   122.01   -11.91  1.90e+00  3.93e+01   6.3*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   128.13   -17.13  2.80e+00  3.74e+01   6.1*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   132.68   -10.98  1.80e+00  3.72e+01   6.1*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   104.38    11.82  2.00e+00  3.50e+01   5.9*sigma
   A 130  SER  O
   A 130  SER  C
   A 131  ILE  N         123.00   113.59     9.41  1.60e+00  3.46e+01   5.9*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   131.46    -9.76  1.80e+00  2.94e+01   5.4*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  C         111.00   125.97   -14.97  2.80e+00  2.86e+01   5.3*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   119.45    -8.95  1.70e+00  2.77e+01   5.3*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   102.56     8.94  1.70e+00  2.77e+01   5.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   124.79    -7.89  1.50e+00  2.77e+01   5.3*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   112.31     9.39  1.80e+00  2.72e+01   5.2*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   119.36    -8.86  1.70e+00  2.71e+01   5.2*sigma
   A 133  GLU  C
   A 133  GLU  CA
   A 133  GLU  CB        110.10   119.88    -9.78  1.90e+00  2.65e+01   5.1*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   119.14    -8.64  1.70e+00  2.58e+01   5.1*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   122.77    -8.87  1.80e+00  2.43e+01   4.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.47    -4.87  1.00e+00  2.37e+01   4.9*sigma
   A 133  GLU  CB
   A 133  GLU  CG
   A 133  GLU  CD        112.60   120.58    -7.98  1.70e+00  2.20e+01   4.7*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   101.42     8.68  1.90e+00  2.09e+01   4.6*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N         116.20   125.31    -9.11  2.00e+00  2.07e+01   4.6*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.29     5.91  1.30e+00  2.07e+01   4.5*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N         116.20   107.47     8.73  2.00e+00  1.91e+01   4.4*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O         120.80   127.83    -7.03  1.70e+00  1.71e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   103.54     6.96  1.70e+00  1.68e+01   4.1*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   129.05    -7.35  1.80e+00  1.67e+01   4.1*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   116.50     6.50  1.60e+00  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   18.474 (Z=  8.473)
  Mean delta:    2.831 (Z=  1.522)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00    48.37   131.63  5.00e+00  6.93e+02  26.3*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    69.12   110.88  5.00e+00  4.92e+02  22.2*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00    82.75    97.25  5.00e+00  3.78e+02  19.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00    89.61    90.39  5.00e+00  3.27e+02  18.1*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00    97.67    82.33  5.00e+00  2.71e+02  16.5*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   105.11    74.89  5.00e+00  2.24e+02  15.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -105.75   -74.25  5.00e+00  2.21e+02  14.8*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -108.27   -71.73  5.00e+00  2.06e+02  14.3*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   126.51    53.49  5.00e+00  1.14e+02  10.7*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   126.96    53.04  5.00e+00  1.13e+02  10.6*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   132.80    47.20  5.00e+00  8.91e+01   9.4*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -136.16   -43.84  5.00e+00  7.69e+01   8.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA          0.00   -43.08    43.08  5.00e+00  7.42e+01   8.6*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   136.96    43.04  5.00e+00  7.41e+01   8.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   148.75    31.25  5.00e+00  3.91e+01   6.2*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -153.63   -26.37  5.00e+00  2.78e+01   5.3*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   154.52    25.48  5.00e+00  2.60e+01   5.1*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   157.64    22.36  5.00e+00  2.00e+01   4.5*sigma

  Min. delta:    0.003
  Max. delta:  131.628
  Mean delta:   20.215

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.05     5.56  2.00e-01  7.73e+02  27.8*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.77     5.41  2.00e-01  7.32e+02  27.1*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.41     5.05  2.00e-01  6.38e+02  25.3*sigma
   A 134  HIS  CA
   A 134  HIS  N
   A 134  HIS  C
   A 134  HIS  CB          2.51    -2.45     4.96  2.00e-01  6.15e+02  24.8*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -2.45     4.93  2.00e-01  6.08e+02  24.7*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.33     4.89  2.00e-01  5.97e+02  24.4*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -1.89     4.32  2.00e-01  4.67e+02  21.6*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.68     4.19  2.00e-01  4.38e+02  20.9*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -0.89     3.33  2.00e-01  2.77e+02  16.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.55     2.98  2.00e-01  2.22e+02  14.9*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     0.39     2.12  2.00e-01  1.12e+02  10.6*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53     1.72     0.80  2.00e-01  1.61e+01   4.0*sigma

  Min. delta:    0.000
  Max. delta:    5.560
  Mean delta:    1.127

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O
   A 125  LYS  N             0.067       0.116       44.82   5.8*sigma
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.052       0.099       53.82   4.9*sigma

  Min. delta:    0.000
  Max. delta:    0.096
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    6" pdbres="HIS A  43  conformer  : HE2, HD1 
    6" pdbres="HIS A 134  conformer  : HE2, HD1 
    6" pdbres="HIS A 135  conformer  : HE2, HD1 
    6" pdbres="HIS A 136  conformer  : HE2, HD1 
    6" pdbres="HIS A 137  conformer  : HE2, HD1 
    6" pdbres="HIS A 138  conformer  : HE2, HD1 
    6" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 127  ARG  HA , Angle C-CA-HA, observed: 96.639, delta from target: 12.361
   A  90  SER  HA , Angle N-CA-HA, observed: 97.543, delta from target: 12.457
   A  51  ILE  HA , Angle N-CA-HA, observed: 122.901, delta from target: -12.901
   A 124  ALA  HA , Angle C-CA-HA, observed: 95.969, delta from target: 13.031
   A  92  THR  HA , Angle C-CA-HA, observed: 95.607, delta from target: 13.393
   A  89  TYR  HA , Angle CB-CA-HA, observed: 95.331, delta from target: 13.669
   A 122  ILE  HA , Angle CB-CA-HA, observed: 122.753, delta from target: -13.753
   A  89  TYR  HA , Angle C-CA-HA, observed: 94.901, delta from target: 14.099
   A 131  ILE  HB , Angle CG2-CB-HB, observed: 123.664, delta from target: -14.664
   A 122  ILE  HA , Angle C-CA-HA, observed: 93.662, delta from target: 15.338
   A 122  ILE  HA , Angle N-CA-HA, observed: 94.572, delta from target: 15.428
   A 131  ILE  HA , Angle C-CA-HA, observed: 93.107, delta from target: 15.893
   A  78  ILE  HA , Angle N-CA-HA, observed: 93.037, delta from target: 16.963
   A  81  TYR  HA , Angle C-CA-HA, observed: 90.121, delta from target: 18.879
   A  51  ILE  HA , Angle C-CA-HA, observed: 81.376, delta from target: 27.624
   A  81  TYR  HA , Angle CB-CA-HA, observed: 80.489, delta from target: 28.511
   A  51  ILE  HA , Angle CB-CA-HA, observed: 79.055, delta from target: 29.945
   A  78  ILE  HA , Angle C-CA-HA, observed: 76.920, delta from target: 32.080

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.096   2242  Z= 0.587
    Angle     :  2.670  32.080   4079  Z= 1.154
    Chirality :  1.127   5.560    176
    Planarity :  0.014   0.089    327
    Dihedral  : 16.387 131.628    769
    Min Nonbonded Distance : 1.469
  
  Molprobity Statistics.
    All-atom Clashscore : 13.98
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  : 10.95 %
      Favored  : 82.48 %
    Rotamer:
      Outliers :  8.06 %
      Allowed  :  4.84 %
      Favored  : 87.10 %
    Cbeta Deviations : 11.36 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 11.45 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.14 (0.62), residues: 137
    helix: -2.12 (0.47), residues: 75
    sheet:  None (None), residues: 0
    loop : -1.89 (0.77), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.047   0.013   PHE A  45 
   TYR   0.209   0.029   TYR A  50 
   ARG   0.035   0.007   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.036   0.012   PHE A  45 
   TYR   0.173   0.032   TYR A  50 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 1.02, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.969, 75.413, 48.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   6.57 %
                favored =  82.48 %
  Rotamer outliers      =   8.06 %
  C-beta deviations     =    15
  Clashscore            =  13.98
  RMS(bonds)            =   0.0115
  RMS(angles)           =   2.67
  MolProbity score      =   3.04

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  89.78 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0090
  RMS(angles)           =   1.80
  MolProbity score      =   2.28

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.565)
  Mean delta:    0.001 (Z=  0.063)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.609 (Z=  1.380)
  Mean delta:    0.376 (Z=  0.206)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   88.434
  Mean delta:   23.019

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.096
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.046
    Angle     :  0.980   4.873   4077  Z= 0.342
    Chirality :  0.035   0.096    176
    Planarity :  0.000   0.001    326
    Dihedral  : 17.935  88.434    768
    Min Nonbonded Distance : 1.462
  
  Molprobity Statistics.
    All-atom Clashscore : 23.91
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  : 17.52 %
      Favored  : 80.29 %
    Rotamer:
      Outliers : 23.39 %
      Allowed  : 17.74 %
      Favored  : 58.87 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.59 (0.47), residues: 137
    helix: -4.04 (0.36), residues: 63
    sheet:  None (None), residues: 0
    loop : -4.90 (0.55), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.003   0.001   TYR A  91 
   ARG   0.001   0.000   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   TYR A  91 
   ARG   0.000   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 134  HIS

=================================== Summary ===================================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2202
     H or D atoms   : 1090
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 139  HIS  C
   A 139  HIS  OXT         1.23    45.78   -44.55  2.00e-02  4.96e+06  2227.6*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     7.57    -6.11  1.90e-02  1.03e+05  321.6*sigma
   A 128  MET  CA
   A 128  MET  C           1.52     7.77    -6.25  2.10e-02  8.85e+04  297.5*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     6.94    -5.49  1.90e-02  8.34e+04  288.8*sigma
   A 128  MET  CA
   A 128  MET  CB          1.53     5.81    -4.28  2.00e-02  4.59e+04  214.1*sigma
   A 126  VAL  N
   A 126  VAL  CA          1.46     2.23    -0.77  1.90e-02  1.63e+03  40.4*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.83    -0.50  1.40e-02  1.27e+03  35.6*sigma
   A  89  TYR  C
   A  90  SER  N           1.33     1.81    -0.48  1.40e-02  1.19e+03  34.5*sigma
   A  76  SER  C
   A  77  ILE  N           1.33     1.75    -0.43  1.40e-02  9.23e+02  30.4*sigma
   A  77  ILE  N
   A  77  ILE  CA          1.46     2.01    -0.55  1.90e-02  8.53e+02  29.2*sigma
   A 125  LYS  N
   A 125  LYS  CA          1.46     2.01    -0.55  1.90e-02  8.44e+02  29.1*sigma
   A 124  ALA  N
   A 124  ALA  CA          1.46     1.94    -0.48  1.90e-02  6.40e+02  25.3*sigma
   A 129  ARG  N
   A 129  ARG  CA          1.46     1.94    -0.48  1.90e-02  6.38e+02  25.3*sigma
   A 130  SER  CA
   A 130  SER  C           1.52     2.00    -0.48  2.10e-02  5.13e+02  22.7*sigma
   A 126  VAL  CA
   A 126  VAL  C           1.52     1.09     0.44  2.10e-02  4.35e+02  20.9*sigma
   A  89  TYR  N
   A  89  TYR  CA          1.46     1.83    -0.37  1.90e-02  3.82e+02  19.6*sigma
   A  88  ASP  C
   A  89  TYR  N           1.33     1.59    -0.26  1.40e-02  3.37e+02  18.4*sigma
   A  79  LYS  CA
   A  79  LYS  C           1.52     1.89    -0.36  2.10e-02  3.01e+02  17.4*sigma
   A  93  LEU  CA
   A  93  LEU  C           1.52     1.86    -0.34  2.10e-02  2.60e+02  16.1*sigma
   A 132  LEU  N
   A 132  LEU  CA          1.46     1.75    -0.30  1.90e-02  2.42e+02  15.5*sigma
   A 128  MET  C
   A 129  ARG  N           1.33     1.54    -0.21  1.40e-02  2.22e+02  14.9*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.12     0.21  1.40e-02  2.21e+02  14.9*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.12     0.21  1.40e-02  2.17e+02  14.7*sigma
   A 122  ILE  CA
   A 122  ILE  CB          1.54     1.92    -0.38  2.70e-02  2.01e+02  14.2*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.73    -0.27  1.90e-02  2.01e+02  14.2*sigma
   A 124  ALA  C
   A 125  LYS  N           1.33     1.15     0.18  1.40e-02  1.63e+02  12.8*sigma
   A 119  LEU  C
   A 120  GLU  N           1.33     1.15     0.18  1.40e-02  1.57e+02  12.5*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.27     0.25  2.10e-02  1.45e+02  12.0*sigma
   A  97  SER  C
   A  98  SER  N           1.33     1.16     0.17  1.40e-02  1.44e+02  12.0*sigma
   A 131  ILE  CA
   A 131  ILE  C           1.52     1.77    -0.25  2.10e-02  1.37e+02  11.7*sigma
   A  92  THR  C
   A  93  LEU  N           1.33     1.49    -0.16  1.40e-02  1.36e+02  11.7*sigma
   A  76  SER  CA
   A  76  SER  C           1.52     1.76    -0.24  2.10e-02  1.30e+02  11.4*sigma
   A 122  ILE  CA
   A 122  ILE  C           1.52     1.29     0.24  2.10e-02  1.27e+02  11.3*sigma
   A 119  LEU  CA
   A 119  LEU  C           1.52     1.31     0.22  2.10e-02  1.10e+02  10.5*sigma
   A  74  ASP  N
   A  74  ASP  CA          1.46     1.27     0.19  1.90e-02  9.99e+01  10.0*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.73    -0.21  2.10e-02  9.82e+01   9.9*sigma
   A 123  GLU  N
   A 123  GLU  CA          1.46     1.65    -0.19  1.90e-02  9.80e+01   9.9*sigma
   A 127  ARG  C
   A 128  MET  N           1.33     1.20     0.13  1.40e-02  8.83e+01   9.4*sigma
   A 127  ARG  CA
   A 127  ARG  C           1.52     1.33     0.20  2.10e-02  8.71e+01   9.3*sigma
   A  28  GLN  C
   A  29  ASP  N           1.33     1.46    -0.13  1.40e-02  8.41e+01   9.2*sigma
   A  93  LEU  N
   A  93  LEU  CA          1.46     1.63    -0.17  1.90e-02  8.17e+01   9.0*sigma
   A 120  GLU  N
   A 120  GLU  CA          1.46     1.29     0.17  1.90e-02  7.74e+01   8.8*sigma
   A  83  THR  C
   A  84  GLU  N           1.33     1.21     0.12  1.40e-02  7.72e+01   8.8*sigma
   A  97  SER  CA
   A  97  SER  C           1.52     1.35     0.17  2.10e-02  6.88e+01   8.3*sigma
   A 123  GLU  C
   A 124  ALA  N           1.33     1.44    -0.12  1.40e-02  6.86e+01   8.3*sigma
   A 132  LEU  C
   A 133  GLU  N           1.33     1.21     0.12  1.40e-02  6.78e+01   8.2*sigma
   A  99  LEU  C
   A 100  GLN  N           1.33     1.21     0.11  1.40e-02  6.66e+01   8.2*sigma
   A  79  LYS  CA
   A  79  LYS  CB          1.53     1.69    -0.16  2.00e-02  6.44e+01   8.0*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.66    -0.14  1.80e-02  6.41e+01   8.0*sigma
   A 119  LEU  CA
   A 119  LEU  CB          1.53     1.69    -0.16  2.00e-02  6.40e+01   8.0*sigma
   A 125  LYS  CA
   A 125  LYS  C           1.52     1.36     0.17  2.10e-02  6.37e+01   8.0*sigma
   A 131  ILE  C
   A 132  LEU  N           1.33     1.22     0.11  1.40e-02  6.02e+01   7.8*sigma
   A  82  THR  C
   A  83  THR  N           1.33     1.22     0.11  1.40e-02  5.70e+01   7.5*sigma
   A  70  LEU  N
   A  70  LEU  CA          1.46     1.60    -0.14  1.90e-02  5.39e+01   7.3*sigma
   A  98  SER  CA
   A  98  SER  C           1.52     1.38     0.15  2.10e-02  4.91e+01   7.0*sigma
   A  98  SER  N
   A  98  SER  CA          1.46     1.33     0.13  1.90e-02  4.63e+01   6.8*sigma
   A  90  SER  N
   A  90  SER  CA          1.46     1.59    -0.13  1.90e-02  4.56e+01   6.8*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.66    -0.13  2.10e-02  4.02e+01   6.3*sigma
   A  93  LEU  C
   A  94  GLY  N           1.33     1.42    -0.09  1.40e-02  4.02e+01   6.3*sigma
   A  35  ALA  C
   A  36  ASP  N           1.33     1.42    -0.09  1.40e-02  3.97e+01   6.3*sigma
   A  96  GLY  C
   A  97  SER  N           1.33     1.42    -0.09  1.40e-02  3.88e+01   6.2*sigma
   A  91  TYR  CA
   A  91  TYR  C           1.52     1.39     0.13  2.10e-02  3.88e+01   6.2*sigma
   A  78  ILE  N
   A  78  ILE  CA          1.46     1.34     0.12  1.90e-02  3.69e+01   6.1*sigma
   A  99  LEU  N
   A  99  LEU  CA          1.46     1.35     0.11  1.90e-02  3.53e+01   5.9*sigma
   A  89  TYR  CA
   A  89  TYR  C           1.52     1.65    -0.12  2.10e-02  3.52e+01   5.9*sigma
   A  29  ASP  N
   A  29  ASP  CA          1.46     1.57    -0.11  1.90e-02  3.48e+01   5.9*sigma
   A 119  LEU  CB
   A 119  LEU  CG          1.53     1.64    -0.11  2.00e-02  2.96e+01   5.4*sigma
   A  98  SER  C
   A  99  LEU  N           1.33     1.25     0.08  1.40e-02  2.96e+01   5.4*sigma
   A  79  LYS  C
   A  80  GLY  N           1.33     1.40    -0.08  1.40e-02  2.88e+01   5.4*sigma
   A 119  LEU  N
   A 119  LEU  CA          1.46     1.56    -0.10  1.90e-02  2.81e+01   5.3*sigma
   A 122  ILE  C
   A 123  GLU  N           1.33     1.40    -0.07  1.40e-02  2.76e+01   5.3*sigma
   A 122  ILE  CB
   A 122  ILE  CG1         1.53     1.63    -0.10  2.00e-02  2.44e+01   4.9*sigma
   A  91  TYR  N
   A  91  TYR  CA          1.46     1.36     0.09  1.90e-02  2.42e+01   4.9*sigma
   A  90  SER  C
   A  91  TYR  N           1.33     1.26     0.07  1.40e-02  2.41e+01   4.9*sigma
   A  70  LEU  CA
   A  70  LEU  C           1.52     1.42     0.10  2.10e-02  2.31e+01   4.8*sigma
   A  91  TYR  C
   A  92  THR  N           1.33     1.26     0.07  1.40e-02  2.27e+01   4.8*sigma
   A 129  ARG  NE
   A 129  ARG  CZ          1.33     1.38    -0.05  1.10e-02  2.26e+01   4.8*sigma
   A  79  LYS  CB
   A  79  LYS  CG          1.52     1.66    -0.14  3.00e-02  2.26e+01   4.8*sigma
   A 123  GLU  CA
   A 123  GLU  C           1.52     1.43     0.10  2.10e-02  2.23e+01   4.7*sigma
   A 126  VAL  CA
   A 126  VAL  CB          1.54     1.66    -0.12  2.70e-02  2.07e+01   4.5*sigma
   A 106  ALA  C
   A 107  LEU  N           1.33     1.39    -0.06  1.40e-02  2.06e+01   4.5*sigma
   A  88  ASP  N
   A  88  ASP  CA          1.46     1.54    -0.09  1.90e-02  2.03e+01   4.5*sigma
   A 109  LYS  N
   A 109  LYS  CA          1.46     1.54    -0.08  1.90e-02  1.86e+01   4.3*sigma
   A 125  LYS  C
   A 126  VAL  N           1.33     1.27     0.06  1.40e-02  1.75e+01   4.2*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.52    -0.07  1.60e-02  1.69e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   44.552 (Z=2227.615)
  Mean delta:    1.365 (Z= 68.334)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10     5.08   105.02  1.90e+00  3.06e+03  55.3*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70    29.88    91.82  1.80e+00  2.60e+03  51.0*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70    32.97    88.73  1.80e+00  2.43e+03  49.3*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N         116.20    20.55    95.65  2.00e+00  2.29e+03  47.8*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  CB        110.50    32.07    78.43  1.70e+00  2.13e+03  46.1*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70    42.99    78.71  1.80e+00  1.91e+03  43.7*sigma
   A  92  THR  O
   A  92  THR  C
   A  93  LEU  N         123.00    55.36    67.64  1.60e+00  1.79e+03  42.3*sigma
   A 125  LYS  O
   A 125  LYS  C
   A 126  VAL  N         123.00    55.90    67.10  1.60e+00  1.76e+03  41.9*sigma
   A 130  SER  O
   A 130  SER  C
   A 131  ILE  N         123.00    57.74    65.26  1.60e+00  1.66e+03  40.8*sigma
   A  51  ILE  O
   A  51  ILE  C
   A  52  PRO  N         123.00    61.05    61.95  1.60e+00  1.50e+03  38.7*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70    53.14    68.56  1.80e+00  1.45e+03  38.1*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50    47.94    63.56  1.70e+00  1.40e+03  37.4*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20    48.99    67.21  2.00e+00  1.13e+03  33.6*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50    58.63    52.87  1.70e+00  9.67e+02  31.1*sigma
   A 128  MET  CA
   A 128  MET  CB
   A 128  MET  CG        114.10    53.37    60.73  2.00e+00  9.22e+02  30.4*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70    67.48    54.22  1.80e+00  9.07e+02  30.1*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    27.36    83.64  2.80e+00  8.92e+02  29.9*sigma
   A 126  VAL  O
   A 126  VAL  C
   A 127  ARG  N         123.00    77.63    45.37  1.60e+00  8.04e+02  28.4*sigma
   A 139  HIS  CA
   A 139  HIS  C
   A 139  HIS  OXT       121.00    36.07    84.93  3.00e+00  8.02e+02  28.3*sigma
   A 119  LEU  O
   A 119  LEU  C
   A 120  GLU  N         123.00   167.31   -44.31  1.60e+00  7.67e+02  27.7*sigma
   A 123  GLU  O
   A 123  GLU  C
   A 124  ALA  N         123.00   164.91   -41.91  1.60e+00  6.86e+02  26.2*sigma
   A 122  ILE  O
   A 122  ILE  C
   A 123  GLU  N         123.00   164.23   -41.23  1.60e+00  6.64e+02  25.8*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    70.09    41.41  1.70e+00  5.93e+02  24.4*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   164.01   -47.81  2.00e+00  5.71e+02  23.9*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N         116.20    69.63    46.57  2.00e+00  5.42e+02  23.3*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    66.18    43.92  1.90e+00  5.34e+02  23.1*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50    72.35    39.15  1.70e+00  5.30e+02  23.0*sigma
   A 131  ILE  O
   A 131  ILE  C
   A 132  LEU  N         123.00    86.59    36.41  1.60e+00  5.18e+02  22.8*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60    90.04    22.56  1.00e+00  5.09e+02  22.6*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70    81.89    39.81  1.80e+00  4.89e+02  22.1*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   160.71   -39.01  1.80e+00  4.70e+02  21.7*sigma
   A  93  LEU  O
   A  93  LEU  C
   A  94  GLY  N         123.00    88.85    34.15  1.60e+00  4.55e+02  21.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   158.46   -42.26  2.00e+00  4.46e+02  21.1*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00    89.80    33.20  1.60e+00  4.31e+02  20.8*sigma
   A 128  MET  CA
   A 128  MET  C
   A 128  MET  O         120.80   155.72   -34.92  1.70e+00  4.22e+02  20.5*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N         116.20    75.59    40.61  2.00e+00  4.12e+02  20.3*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   157.04   -35.34  1.80e+00  3.85e+02  19.6*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70    87.63    34.07  1.80e+00  3.58e+02  18.9*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40    82.25    28.15  1.50e+00  3.52e+02  18.8*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   152.90   -36.70  2.00e+00  3.37e+02  18.4*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG2       110.50    79.84    30.66  1.70e+00  3.25e+02  18.0*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20    80.15    36.05  2.00e+00  3.25e+02  18.0*sigma
   A  91  TYR  O
   A  91  TYR  C
   A  92  THR  N         123.00    94.93    28.07  1.60e+00  3.08e+02  17.5*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50    84.49    26.01  1.50e+00  3.01e+02  17.3*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   139.94   -29.44  1.70e+00  3.00e+02  17.3*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   152.15   -30.45  1.80e+00  2.86e+02  16.9*sigma
   A 127  ARG  O
   A 127  ARG  C
   A 128  MET  N         123.00    96.53    26.47  1.60e+00  2.74e+02  16.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   141.60   -24.70  1.50e+00  2.71e+02  16.5*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    66.19    44.81  2.80e+00  2.56e+02  16.0*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG1       110.40   137.29   -26.89  1.70e+00  2.50e+02  15.8*sigma
   A 130  SER  C
   A 130  SER  CA
   A 130  SER  CB        110.10    80.22    29.88  1.90e+00  2.47e+02  15.7*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  89  TYR  O         120.80    94.42    26.38  1.70e+00  2.41e+02  15.5*sigma
   A 119  LEU  N
   A 119  LEU  CA
   A 119  LEU  CB        110.50    85.42    25.08  1.70e+00  2.18e+02  14.8*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    85.52    24.98  1.70e+00  2.16e+02  14.7*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00    70.41    40.59  2.80e+00  2.10e+02  14.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20    87.28    28.92  2.00e+00  2.09e+02  14.5*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  C         111.00    71.19    39.81  2.80e+00  2.02e+02  14.2*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   146.82   -25.12  1.80e+00  1.95e+02  14.0*sigma
   A  88  ASP  C
   A  88  ASP  CA
   A  88  ASP  CB        110.10    83.81    26.29  1.90e+00  1.92e+02  13.8*sigma
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        121.70    97.54    24.16  1.80e+00  1.80e+02  13.4*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   145.72   -24.02  1.80e+00  1.78e+02  13.3*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20    89.52    26.68  2.00e+00  1.78e+02  13.3*sigma
   A 122  ILE  CG1
   A 122  ILE  CB
   A 122  ILE  CG2       110.70    70.89    39.81  3.00e+00  1.76e+02  13.3*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   102.00    21.00  1.60e+00  1.72e+02  13.1*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  C         111.00    75.07    35.93  2.80e+00  1.65e+02  12.8*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   133.74   -23.64  1.90e+00  1.55e+02  12.4*sigma
   A  90  SER  O
   A  90  SER  C
   A  91  TYR  N         123.00   142.77   -19.77  1.60e+00  1.53e+02  12.4*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50    90.59    20.91  1.70e+00  1.51e+02  12.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N         116.20   140.40   -24.20  2.00e+00  1.46e+02  12.1*sigma
   A  28  GLN  C
   A  29  ASP  N
   A  29  ASP  CA        121.70   100.16    21.54  1.80e+00  1.43e+02  12.0*sigma
   A 119  LEU  N
   A 119  LEU  CA
   A 119  LEU  C         111.00   144.49   -33.49  2.80e+00  1.43e+02  12.0*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20    92.31    23.89  2.00e+00  1.43e+02  11.9*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  C         111.00    77.73    33.27  2.80e+00  1.41e+02  11.9*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   124.38   -11.78  1.00e+00  1.39e+02  11.8*sigma
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        121.70   100.62    21.08  1.80e+00  1.37e+02  11.7*sigma
   A 119  LEU  C
   A 119  LEU  CA
   A 119  LEU  CB        110.10    87.91    22.19  1.90e+00  1.36e+02  11.7*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50    91.49    19.01  1.70e+00  1.25e+02  11.2*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   101.57    20.13  1.80e+00  1.25e+02  11.2*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    89.03    21.07  1.90e+00  1.23e+02  11.1*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   135.63   -21.53  2.00e+00  1.16e+02  10.8*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  93  LEU  O         120.80   139.05   -18.25  1.70e+00  1.15e+02  10.7*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  CB        110.50    92.42    18.08  1.70e+00  1.13e+02  10.6*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  CB        110.50    92.64    17.86  1.70e+00  1.10e+02  10.5*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   137.01   -20.81  2.00e+00  1.08e+02  10.4*sigma
   A  83  THR  O
   A  83  THR  C
   A  84  GLU  N         123.00   106.36    16.64  1.60e+00  1.08e+02  10.4*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  CB        110.50    92.84    17.66  1.70e+00  1.08e+02  10.4*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60    94.06    15.54  1.50e+00  1.07e+02  10.4*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  C         111.00    82.44    28.56  2.80e+00  1.04e+02  10.2*sigma
   A  78  ILE  O
   A  78  ILE  C
   A  79  LYS  N         123.00   106.94    16.06  1.60e+00  1.01e+02  10.0*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   127.55   -17.05  1.70e+00  1.01e+02  10.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   104.08    16.72  1.70e+00  9.67e+01   9.8*sigma
   A 139  HIS  O
   A 139  HIS  C
   A 139  HIS  OXT       118.00    88.75    29.25  3.00e+00  9.51e+01   9.8*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   139.12   -17.42  1.80e+00  9.36e+01   9.7*sigma
   A  94  GLY  O
   A  94  GLY  C
   A  95  ASP  N         123.00   138.33   -15.33  1.60e+00  9.18e+01   9.6*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60    92.55    19.05  2.00e+00  9.07e+01   9.5*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  88  ASP  O         120.80   104.80    16.00  1.70e+00  8.86e+01   9.4*sigma
   A 120  GLU  O
   A 120  GLU  C
   A 121  GLY  N         123.00   137.68   -14.68  1.60e+00  8.42e+01   9.2*sigma
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   105.44    16.26  1.80e+00  8.16e+01   9.0*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  C         111.00   136.05   -25.05  2.80e+00  8.00e+01   8.9*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   137.76   -16.06  1.80e+00  7.96e+01   8.9*sigma
   A  35  ALA  C
   A  36  ASP  N
   A  36  ASP  CA        121.70   105.70    16.00  1.80e+00  7.90e+01   8.9*sigma
   A 132  LEU  N
   A 132  LEU  CA
   A 132  LEU  CB        110.50   125.56   -15.06  1.70e+00  7.85e+01   8.9*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N         116.20    98.72    17.48  2.00e+00  7.64e+01   8.7*sigma
   A  70  LEU  N
   A  70  LEU  CA
   A  70  LEU  CB        110.50    95.71    14.79  1.70e+00  7.57e+01   8.7*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50    96.13    14.37  1.70e+00  7.14e+01   8.5*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  CB        110.50    96.22    14.28  1.70e+00  7.05e+01   8.4*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   130.53   -19.23  2.30e+00  6.99e+01   8.4*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   109.67    13.33  1.60e+00  6.95e+01   8.3*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00    87.70    23.30  2.80e+00  6.92e+01   8.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  76  SER  O         120.80   107.26    13.54  1.70e+00  6.35e+01   8.0*sigma
   A  98  SER  O
   A  98  SER  C
   A  99  LEU  N         123.00   135.68   -12.68  1.60e+00  6.28e+01   7.9*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50    97.10    13.40  1.70e+00  6.22e+01   7.9*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40    97.06    13.34  1.70e+00  6.16e+01   7.8*sigma
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        121.70   107.59    14.11  1.80e+00  6.15e+01   7.8*sigma
   A  76  SER  O
   A  76  SER  C
   A  77  ILE  N         123.00   110.65    12.35  1.60e+00  5.96e+01   7.7*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD2       120.80   109.35    11.45  1.50e+00  5.83e+01   7.6*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 131  ILE  O         120.80   133.77   -12.97  1.70e+00  5.82e+01   7.6*sigma
   A  88  ASP  O
   A  88  ASP  C
   A  89  TYR  N         123.00   110.81    12.19  1.60e+00  5.80e+01   7.6*sigma
   A 123  GLU  CA
   A 123  GLU  CB
   A 123  GLU  CG        114.10    98.94    15.16  2.00e+00  5.75e+01   7.6*sigma
   A 129  ARG  CG
   A 129  ARG  CD
   A 129  ARG  NE        112.00   128.60   -16.60  2.20e+00  5.69e+01   7.5*sigma
   A 132  LEU  C
   A 132  LEU  CA
   A 132  LEU  CB        110.10    96.09    14.01  1.90e+00  5.43e+01   7.4*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   134.91   -13.21  1.80e+00  5.39e+01   7.3*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   131.48   -20.48  2.80e+00  5.35e+01   7.3*sigma
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        121.70   108.61    13.09  1.80e+00  5.29e+01   7.3*sigma
   A 119  LEU  CA
   A 119  LEU  CB
   A 119  LEU  CG        116.30   141.13   -24.83  3.50e+00  5.03e+01   7.1*sigma
   A  83  THR  N
   A  83  THR  CA
   A  83  THR  C         111.00   130.87   -19.87  2.80e+00  5.03e+01   7.1*sigma
   A  76  SER  N
   A  76  SER  CA
   A  76  SER  C         111.00   130.80   -19.80  2.80e+00  5.00e+01   7.1*sigma
   A  80  GLY  N
   A  80  GLY  CA
   A  80  GLY  C         113.30    92.95    20.35  2.90e+00  4.93e+01   7.0*sigma
   A  97  SER  O
   A  97  SER  C
   A  98  SER  N         123.00   134.19   -11.19  1.60e+00  4.89e+01   7.0*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   134.25   -12.55  1.80e+00  4.86e+01   7.0*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N         116.20   130.00   -13.80  2.00e+00  4.76e+01   6.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   109.07    11.73  1.70e+00  4.76e+01   6.9*sigma
   A 125  LYS  C
   A 125  LYS  CA
   A 125  LYS  CB        110.10   122.97   -12.87  1.90e+00  4.59e+01   6.8*sigma
   A 131  ILE  CG1
   A 131  ILE  CB
   A 131  ILE  CG2       110.70    90.39    20.31  3.00e+00  4.59e+01   6.8*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N         116.20   102.80    13.40  2.00e+00  4.49e+01   6.7*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  C         111.00    92.26    18.74  2.80e+00  4.48e+01   6.7*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N         116.20   102.85    13.35  2.00e+00  4.45e+01   6.7*sigma
   A  22  PRO  N
   A  22  PRO  CA
   A  22  PRO  CB        103.00   110.30    -7.30  1.10e+00  4.40e+01   6.6*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O         120.80   131.99   -11.19  1.70e+00  4.33e+01   6.6*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50    99.32    11.18  1.70e+00  4.32e+01   6.6*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG1       110.40   121.57   -11.17  1.70e+00  4.31e+01   6.6*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N         116.20   103.13    13.07  2.00e+00  4.27e+01   6.5*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10    94.90    14.20  2.20e+00  4.17e+01   6.5*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10    97.96    12.14  1.90e+00  4.08e+01   6.4*sigma
   A 106  ALA  C
   A 107  LEU  N
   A 107  LEU  CA        121.70   110.24    11.46  1.80e+00  4.05e+01   6.4*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  94  GLY  O         120.80   107.53    13.27  2.10e+00  4.00e+01   6.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   110.07    10.73  1.70e+00  3.99e+01   6.3*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   121.15   -10.65  1.70e+00  3.93e+01   6.3*sigma
   A  42  GLY  O
   A  42  GLY  C
   A  43  HIS  N         123.00   113.05     9.95  1.60e+00  3.87e+01   6.2*sigma
   A 130  SER  CA
   A 130  SER  C
   A 130  SER  O         120.80   131.33   -10.53  1.70e+00  3.84e+01   6.2*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  CB        110.50   100.00    10.50  1.70e+00  3.81e+01   6.2*sigma
   A 120  GLU  N
   A 120  GLU  CA
   A 120  GLU  C         111.00    93.73    17.27  2.80e+00  3.80e+01   6.2*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   128.48   -12.28  2.00e+00  3.77e+01   6.1*sigma
   A  98  SER  CA
   A  98  SER  CB
   A  98  SER  OG        111.10    99.19    11.91  2.00e+00  3.55e+01   6.0*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80    97.71    13.09  2.20e+00  3.54e+01   6.0*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N         116.20   104.38    11.82  2.00e+00  3.49e+01   5.9*sigma
   A 108  ILE  C
   A 109  LYS  N
   A 109  LYS  CA        121.70   111.11    10.59  1.80e+00  3.46e+01   5.9*sigma
   A  79  LYS  CG
   A  79  LYS  CD
   A  79  LYS  CE        111.30   124.60   -13.30  2.30e+00  3.35e+01   5.8*sigma
   A  22  PRO  C
   A  22  PRO  CA
   A  22  PRO  CB        110.10   120.99   -10.89  1.90e+00  3.28e+01   5.7*sigma
   A  98  SER  C
   A  98  SER  CA
   A  98  SER  CB        110.10    99.25    10.85  1.90e+00  3.26e+01   5.7*sigma
   A 133  GLU  O
   A 133  GLU  C
   A 134  HIS  N         123.00   113.89     9.11  1.60e+00  3.24e+01   5.7*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   131.93   -10.23  1.80e+00  3.23e+01   5.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O         120.80   111.20     9.60  1.70e+00  3.19e+01   5.6*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  C         111.00   126.66   -15.66  2.80e+00  3.13e+01   5.6*sigma
   A  29  ASP  N
   A  29  ASP  CA
   A  29  ASP  CB        110.50   101.12     9.38  1.70e+00  3.04e+01   5.5*sigma
   A  59  LEU  C
   A  60  ALA  N
   A  60  ALA  CA        121.70   111.81     9.89  1.80e+00  3.02e+01   5.5*sigma
   A 129  ARG  NE
   A 129  ARG  CZ
   A 129  ARG  NH2       119.20   124.13    -4.93  9.00e-01  3.00e+01   5.5*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10    99.78    10.32  1.90e+00  2.95e+01   5.4*sigma
   A 119  LEU  CD1
   A 119  LEU  CG
   A 119  LEU  CD2       110.80    99.00    11.80  2.20e+00  2.88e+01   5.4*sigma
   A  67  PHE  C
   A  68  TYR  N
   A  68  TYR  CA        121.70   112.09     9.61  1.80e+00  2.85e+01   5.3*sigma
   A  80  GLY  O
   A  80  GLY  C
   A  81  TYR  N         123.00   114.53     8.47  1.60e+00  2.80e+01   5.3*sigma
   A  22  PRO  N
   A  22  PRO  CA
   A  22  PRO  C         112.10   125.28   -13.18  2.50e+00  2.78e+01   5.3*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  C         112.10   125.16   -13.06  2.50e+00  2.73e+01   5.2*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   108.67    -5.67  1.10e+00  2.66e+01   5.2*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   126.39   -10.19  2.00e+00  2.60e+01   5.1*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N         116.20   106.04    10.16  2.00e+00  2.58e+01   5.1*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N         116.20   126.34   -10.14  2.00e+00  2.57e+01   5.1*sigma
   A  25  LEU  O
   A  25  LEU  C
   A  26  LEU  N         123.00   114.90     8.10  1.60e+00  2.56e+01   5.1*sigma
   A  64  LEU  C
   A  65  SER  N
   A  65  SER  CA        121.70   112.61     9.09  1.80e+00  2.55e+01   5.1*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N         116.20   106.15    10.05  2.00e+00  2.53e+01   5.0*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   126.24   -10.04  2.00e+00  2.52e+01   5.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  90  SER  O         120.80   129.28    -8.48  1.70e+00  2.49e+01   5.0*sigma
   A  96  GLY  O
   A  96  GLY  C
   A  97  SER  N         123.00   130.94    -7.94  1.60e+00  2.46e+01   5.0*sigma
   A  96  GLY  N
   A  96  GLY  CA
   A  96  GLY  C         113.30    98.97    14.33  2.90e+00  2.44e+01   4.9*sigma
   A  70  LEU  C
   A  71  ILE  N
   A  71  ILE  CA        121.70   112.87     8.83  1.80e+00  2.41e+01   4.9*sigma
   A  87  GLY  N
   A  87  GLY  CA
   A  87  GLY  C         113.30    99.29    14.01  2.90e+00  2.34e+01   4.8*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 122  ILE  O         120.80   112.61     8.19  1.70e+00  2.32e+01   4.8*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   124.48   -13.48  2.80e+00  2.32e+01   4.8*sigma
   A  27  LYS  CA
   A  27  LYS  CB
   A  27  LYS  CG        114.10   104.49     9.61  2.00e+00  2.31e+01   4.8*sigma
   A 104  VAL  CG1
   A 104  VAL  CB
   A 104  VAL  CG2       110.80   100.29    10.51  2.20e+00  2.28e+01   4.8*sigma
   A  95  ASP  N
   A  95  ASP  CA
   A  95  ASP  CB        110.50   118.61    -8.11  1.70e+00  2.27e+01   4.8*sigma
   A  33  ALA  N
   A  33  ALA  CA
   A  33  ALA  CB        110.40   103.25     7.15  1.50e+00  2.27e+01   4.8*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00    97.72    13.28  2.80e+00  2.25e+01   4.7*sigma
   A  36  ASP  N
   A  36  ASP  CA
   A  36  ASP  CB        110.50   102.45     8.05  1.70e+00  2.24e+01   4.7*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   119.07    -8.97  1.90e+00  2.23e+01   4.7*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N         116.20   106.86     9.34  2.00e+00  2.18e+01   4.7*sigma
   A 104  VAL  CA
   A 104  VAL  CB
   A 104  VAL  CG1       110.40   102.51     7.89  1.70e+00  2.15e+01   4.6*sigma
   A  83  THR  N
   A  83  THR  CA
   A  83  THR  CB        111.50   103.66     7.84  1.70e+00  2.12e+01   4.6*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   113.46     8.24  1.80e+00  2.10e+01   4.6*sigma
   A  76  SER  C
   A  76  SER  CA
   A  76  SER  CB        110.10   118.73    -8.63  1.90e+00  2.06e+01   4.5*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   125.16    -8.96  2.00e+00  2.01e+01   4.5*sigma
   A  52  PRO  C
   A  52  PRO  CA
   A  52  PRO  CB        110.10   118.57    -8.47  1.90e+00  1.99e+01   4.5*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    98.54    12.46  2.80e+00  1.98e+01   4.5*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   129.70    -8.00  1.80e+00  1.97e+01   4.4*sigma
   A  33  ALA  O
   A  33  ALA  C
   A  34  THR  N         123.00   130.07    -7.07  1.60e+00  1.95e+01   4.4*sigma
   A   1  MET  CA
   A   1  MET  CB
   A   1  MET  CG        114.10   105.30     8.80  2.00e+00  1.94e+01   4.4*sigma
   A  39  LEU  N
   A  39  LEU  CA
   A  39  LEU  CB        110.50   103.02     7.48  1.70e+00  1.93e+01   4.4*sigma
   A  98  SER  CA
   A  98  SER  C
   A  98  SER  O         120.80   113.34     7.46  1.70e+00  1.93e+01   4.4*sigma
   A  95  ASP  C
   A  95  ASP  CA
   A  95  ASP  CB        110.10   118.42    -8.32  1.90e+00  1.92e+01   4.4*sigma
   A 129  ARG  CA
   A 129  ARG  CB
   A 129  ARG  CG        114.10   105.38     8.72  2.00e+00  1.90e+01   4.4*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   129.53    -7.83  1.80e+00  1.89e+01   4.4*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00    98.91    12.09  2.80e+00  1.87e+01   4.3*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   119.59    -8.19  1.90e+00  1.86e+01   4.3*sigma
   A 121  GLY  N
   A 121  GLY  CA
   A 121  GLY  C         113.30   125.75   -12.45  2.90e+00  1.84e+01   4.3*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  C         111.00    99.04    11.96  2.80e+00  1.82e+01   4.3*sigma
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        122.60   101.44    21.16  5.00e+00  1.79e+01   4.2*sigma
   A  42  GLY  CA
   A  42  GLY  C
   A  42  GLY  O         120.80   111.94     8.86  2.10e+00  1.78e+01   4.2*sigma
   A  40  LYS  O
   A  40  LYS  C
   A  41  VAL  N         123.00   116.29     6.71  1.60e+00  1.76e+01   4.2*sigma
   A 120  GLU  C
   A 120  GLU  CA
   A 120  GLU  CB        110.10   118.07    -7.97  1.90e+00  1.76e+01   4.2*sigma
   A   1  MET  O
   A   1  MET  C
   A   2  LEU  N         123.00   129.69    -6.69  1.60e+00  1.75e+01   4.2*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   106.15     5.85  1.40e+00  1.75e+01   4.2*sigma
   A  60  ALA  O
   A  60  ALA  C
   A  61  LEU  N         123.00   116.33     6.67  1.60e+00  1.74e+01   4.2*sigma
   A  50  TYR  O
   A  50  TYR  C
   A  51  ILE  N         123.00   129.60    -6.60  1.60e+00  1.70e+01   4.1*sigma
   A   1  MET  CA
   A   1  MET  C
   A   2  LEU  N         116.20   107.95     8.25  2.00e+00  1.70e+01   4.1*sigma
   A  99  LEU  O
   A  99  LEU  C
   A 100  GLN  N         123.00   129.52    -6.52  1.60e+00  1.66e+01   4.1*sigma
   A  70  LEU  O
   A  70  LEU  C
   A  71  ILE  N         123.00   129.51    -6.51  1.60e+00  1.66e+01   4.1*sigma
   A  32  GLU  CA
   A  32  GLU  CB
   A  32  GLU  CG        114.10   105.97     8.13  2.00e+00  1.65e+01   4.1*sigma
   A  82  THR  O
   A  82  THR  C
   A  83  THR  N         123.00   116.51     6.49  1.60e+00  1.65e+01   4.1*sigma
   A 125  LYS  CA
   A 125  LYS  CB
   A 125  LYS  CG        114.10   122.20    -8.10  2.00e+00  1.64e+01   4.0*sigma
   A  22  PRO  CA
   A  22  PRO  C
   A  23  ASP  N         116.20   124.21    -8.01  2.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:  105.021 (Z= 55.274)
  Mean delta:   11.511 (Z=  6.137)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   119.39    60.61  5.00e+00  1.47e+02  12.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   146.39    33.61  5.00e+00  4.52e+01   6.7*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -159.57   -20.43  5.00e+00  1.67e+01   4.1*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -159.62   -20.38  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.019
  Max. delta:   85.972
  Mean delta:   18.507

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 130  SER  CA
   A 130  SER  N
   A 130  SER  C
   A 130  SER  CB          2.51    22.67   -20.16  2.00e-01  1.02e+04  100.8*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -5.11     7.59  2.00e-01  1.44e+03  38.0*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -4.00     6.51  2.00e-01  1.06e+03  32.6*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -3.15     5.68  2.00e-01  8.06e+02  28.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -3.09     5.64  2.00e-01  7.95e+02  28.2*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -2.73     5.24  2.00e-01  6.87e+02  26.2*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -2.13     4.56  2.00e-01  5.20e+02  22.8*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -1.09     3.60  2.00e-01  3.23e+02  18.0*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51     5.08    -2.57  2.00e-01  1.65e+02  12.8*sigma
   A  22  PRO  CA
   A  22  PRO  N
   A  22  PRO  C
   A  22  PRO  CB          2.72     0.85     1.87  2.00e-01  8.74e+01   9.3*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51     4.27    -1.76  2.00e-01  7.73e+01   8.8*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.05     1.46  2.00e-01  5.34e+01   7.3*sigma
   A  76  SER  CA
   A  76  SER  N
   A  76  SER  C
   A  76  SER  CB          2.51     1.07     1.44  2.00e-01  5.17e+01   7.2*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  C
   A  52  PRO  CB          2.72     1.31     1.41  2.00e-01  4.97e+01   7.1*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51     3.67    -1.16  2.00e-01  3.36e+01   5.8*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43     3.35    -0.91  2.00e-01  2.08e+01   4.6*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     3.37    -0.86  2.00e-01  1.84e+01   4.3*sigma
   A  82  THR  CA
   A  82  THR  N
   A  82  THR  C
   A  82  THR  CB          2.53     1.73     0.80  2.00e-01  1.60e+01   4.0*sigma
   A  41  VAL  CA
   A  41  VAL  N
   A  41  VAL  C
   A  41  VAL  CB          2.44     1.64     0.80  2.00e-01  1.60e+01   4.0*sigma

  Min. delta:    0.002
  Max. delta:   20.157
  Mean delta:    1.940

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.331       0.614     2191.47  30.7*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  93  LEU  O
   A  94  GLY  N             0.195       0.329      379.75  16.5*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O
   A 127  ARG  N             0.184       0.313      337.13  15.7*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O
   A  52  PRO  N             0.184       0.292      338.85  14.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O
   A  78  ILE  N             0.166       0.286      276.67  14.3*sigma
   A  83  THR  CA
   A  83  THR  C
   A  83  THR  O
   A  84  GLU  N             0.141       0.244      199.09  12.2*sigma
   A 130  SER  CA
   A 130  SER  C
   A 130  SER  O
   A 131  ILE  N             0.256       0.219      655.88  11.0*sigma
   A  97  SER  CA
   A  97  SER  C
   A  97  SER  O
   A  98  SER  N             0.115       0.198      132.25   9.9*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 132  LEU  O
   A 133  GLU  N             0.093       0.161       87.21   8.1*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O
   A  93  LEU  N             0.100       0.153      100.02   7.6*sigma
   A 139  HIS  CA
   A 139  HIS  C
   A 139  HIS  O
   A 139  HIS  OXT           0.094       0.152       88.40   7.6*sigma
   A  98  SER  CA
   A  98  SER  C
   A  98  SER  O
   A  99  LEU  N             0.087       0.150       75.71   7.5*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  78  ILE  O
   A  79  LYS  N             0.082       0.143       68.00   7.1*sigma
   A 107  LEU  CA
   A 107  LEU  C
   A 107  LEU  O
   A 108  ILE  N             0.082       0.142       67.90   7.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O
   A 125  LYS  N             0.158       0.141      249.01   7.1*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  95  ASP  O
   A  96  GLY  N             0.073       0.126       53.25   6.3*sigma
   A 103  ASP  CA
   A 103  ASP  C
   A 103  ASP  O
   A 104  VAL  N             0.071       0.124       51.02   6.2*sigma
   A 110  ASP  CA
   A 110  ASP  C
   A 110  ASP  O
   A 111  TYR  N             0.067       0.116       44.98   5.8*sigma
   A  36  ASP  CA
   A  36  ASP  C
   A  36  ASP  O
   A  37  ILE  N             0.067       0.116       44.79   5.8*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O
   A 128  MET  N             0.184       0.114      338.85   5.7*sigma
   A 128  MET  CA
   A 128  MET  C
   A 128  MET  O
   A 129  ARG  N             0.099       0.112       97.52   5.6*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  73  GLY  O
   A  74  ASP  N             0.065       0.112       41.83   5.6*sigma
   A  27  LYS  CA
   A  27  LYS  C
   A  27  LYS  O
   A  28  GLN  N             0.064       0.111       41.56   5.6*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  87  GLY  O
   A  88  ASP  N             0.064       0.111       41.41   5.6*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  84  GLU  O
   A  85  LYS  N             0.061       0.106       37.77   5.3*sigma
   A  42  GLY  CA
   A  42  GLY  C
   A  42  GLY  O
   A  43  HIS  N             0.164       0.106      269.16   5.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  89  TYR  O
   A  90  SER  N             0.061       0.105       37.25   5.3*sigma
   A  41  VAL  CA
   A  41  VAL  C
   A  41  VAL  O
   A  42  GLY  N             0.059       0.103       35.26   5.1*sigma
   A  74  ASP  CB
   A  74  ASP  CG
   A  74  ASP  OD1
   A  74  ASP  OD2           0.058       0.100       33.12   5.0*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  94  GLY  O
   A  95  ASP  N             0.056       0.097       31.50   4.8*sigma
   A  58  ARG  CA
   A  58  ARG  C
   A  58  ARG  O
   A  59  LEU  N             0.054       0.094       29.65   4.7*sigma
   A   1  MET  CA
   A   1  MET  C
   A   1  MET  O
   A   2  LEU  N             0.054       0.094       29.56   4.7*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.049       0.090       48.90   4.5*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  88  ASP  O
   A  89  TYR  N             0.149       0.089      221.95   4.5*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  91  TYR  O
   A  92  THR  N             0.139       0.089      191.97   4.4*sigma
   A  76  SER  CA
   A  76  SER  C
   A  76  SER  O
   A  77  ILE  N             0.050       0.086       24.69   4.3*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  96  GLY  O
   A  97  SER  N             0.120       0.086      143.45   4.3*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 121  GLY  O
   A 122  ILE  N             0.128       0.084      164.17   4.2*sigma
   A  26  LEU  CA
   A  26  LEU  C
   A  26  LEU  O
   A  27  LYS  N             0.048       0.084       23.33   4.2*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  74  ASP  O
   A  75  GLU  N             0.118       0.083      139.25   4.2*sigma
   A  19  LYS  CA
   A  19  LYS  C
   A  19  LYS  O
   A  20  THR  N             0.047       0.081       22.18   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.331
  Mean delta:    0.068

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1090
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1090
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="ILE A  77  conformer  : H 
    0" pdbres="GLU A  84  conformer  : H 
    0" pdbres="SER A  90  conformer  : H 
    0" pdbres="TYR A  91  conformer  : H 
    0" pdbres="THR A  92  conformer  : HG1 
    0" pdbres="GLY A  94  conformer  : H 
    0" pdbres="GLU A 120  conformer  : H 
    0" pdbres="ILE A 122  conformer  : H 
    0" pdbres="ALA A 124  conformer  : H 
    0" pdbres="LYS A 125  conformer  : H 
    0" pdbres="VAL A 126  conformer  : H 
    0" pdbres="ARG A 127  conformer  : H 
    0" pdbres="MET A 128  conformer  : H 
    0" pdbres="SER A 130  conformer  : H 
    0" pdbres="LEU A 132  conformer  : H 
    0" pdbres="GLU A 133  conformer  : H 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  95  ASP  H  , Angle C-N-H, observed: 136.473, delta from target: -12.173
   A 120  GLU  HA , Angle N-CA-HA, observed: 122.180, delta from target: -12.180
   A  76  SER  HA , Angle N-CA-HA, observed: 97.811, delta from target: 12.189
   A  83  THR  HA , Angle N-CA-HA, observed: 97.763, delta from target: 12.237
   A 109  LYS  HA , Angle N-CA-HA, observed: 97.545, delta from target: 12.455
   A 131  ILE  HA , Angle N-CA-HA, observed: 122.514, delta from target: -12.514
   A 104  VAL  HA , Angle N-CA-HA, observed: 97.007, delta from target: 12.993
   A 128  MET  HB3, Angle CA-CB-HB3, observed: 122.095, delta from target: -13.095
   A 128  MET  HB2, Angle CA-CB-HB2, observed: 122.112, delta from target: -13.112
   A  78  ILE  HB , Angle CA-CB-HB, observed: 122.173, delta from target: -13.173
   A  93  LEU  HA , Angle N-CA-HA, observed: 123.442, delta from target: -13.442
   A 123  GLU  H  , Angle C-N-H, observed: 110.842, delta from target: 13.458
   A  92  THR  HB , Angle OG1-CB-HB, observed: 122.587, delta from target: -13.587
   A 126  VAL  HB , Angle CG1-CB-HB, observed: 121.958, delta from target: -13.958
   A 128  MET  HB3, Angle CG-CB-HB3, observed: 122.111, delta from target: -14.111
   A 128  MET  HB2, Angle CG-CB-HB2, observed: 122.113, delta from target: -14.113
   A  89  TYR  HA , Angle C-CA-HA, observed: 94.839, delta from target: 14.161
   A  79  LYS  HA , Angle CB-CA-HA, observed: 123.214, delta from target: -14.214
   A  89  TYR  H  , Angle CA-N-H, observed: 99.759, delta from target: 14.241
   A  83  THR  HA , Angle C-CA-HA, observed: 94.476, delta from target: 14.524
   A 129  ARG  HA , Angle N-CA-HA, observed: 95.299, delta from target: 14.701
   A 130  SER  HA , Angle CB-CA-HA, observed: 124.351, delta from target: -15.351
   A  95  ASP  HA , Angle CB-CA-HA, observed: 93.564, delta from target: 15.436
   A  97  SER  HA , Angle CB-CA-HA, observed: 93.299, delta from target: 15.701
   A 127  ARG  HA , Angle C-CA-HA, observed: 92.791, delta from target: 16.209
   A  89  TYR  H  , Angle C-N-H, observed: 108.091, delta from target: 16.209
   A  93  LEU  H  , Angle CA-N-H, observed: 130.725, delta from target: -16.725
   A 119  LEU  HG , Angle CB-CG-HG, observed: 92.202, delta from target: 16.798
   A  89  TYR  HA , Angle CB-CA-HA, observed: 125.874, delta from target: -16.874
   A  93  LEU  H  , Angle C-N-H, observed: 141.643, delta from target: -17.343
   A  83  THR  HA , Angle CB-CA-HA, observed: 126.547, delta from target: -17.547
   A  76  SER  HA , Angle CB-CA-HA, observed: 126.653, delta from target: -17.653
   A 127  ARG  HA , Angle CB-CA-HA, observed: 126.866, delta from target: -17.866
   A  78  ILE  HA , Angle C-CA-HA, observed: 127.095, delta from target: -18.095
   A 129  ARG  HA , Angle CB-CA-HA, observed: 90.753, delta from target: 18.247
   A  97  SER  HA , Angle C-CA-HA, observed: 127.269, delta from target: -18.269
   A  74  ASP  HA , Angle N-CA-HA, observed: 128.435, delta from target: -18.435
   A 122  ILE  HA , Angle C-CA-HA, observed: 90.548, delta from target: 18.452
   A 124  ALA  HA , Angle CB-CA-HA, observed: 128.090, delta from target: -19.090
   A  92  THR  H  , Angle CA-N-H, observed: 133.504, delta from target: -19.504
   A  92  THR  H  , Angle C-N-H, observed: 144.607, delta from target: -20.307
   A 123  GLU  HA , Angle N-CA-HA, observed: 130.359, delta from target: -20.359
   A  92  THR  HA , Angle CB-CA-HA, observed: 129.721, delta from target: -20.721
   A  98  SER  HA , Angle CB-CA-HA, observed: 129.876, delta from target: -20.876
   A  93  LEU  HA , Angle CB-CA-HA, observed: 130.331, delta from target: -21.331
   A 130  SER  HA , Angle C-CA-HA, observed: 130.332, delta from target: -21.332
   A 126  VAL  HA , Angle CB-CA-HA, observed: 132.318, delta from target: -23.318
   A 124  ALA  HA , Angle C-CA-HA, observed: 132.788, delta from target: -23.788
   A 124  ALA  HA , Angle N-CA-HA, observed: 134.274, delta from target: -24.274
   A  52  PRO  HA , Angle C-CA-HA, observed: 83.780, delta from target: 25.220
   A 132  LEU  HA , Angle N-CA-HA, observed: 84.712, delta from target: 25.288
   A 122  ILE  HA , Angle N-CA-HA, observed: 135.454, delta from target: -25.454
   A 125  LYS  HA , Angle N-CA-HA, observed: 136.027, delta from target: -26.027
   A  79  LYS  HA , Angle C-CA-HA, observed: 135.265, delta from target: -26.265
   A 122  ILE  HA , Angle CB-CA-HA, observed: 135.750, delta from target: -26.750
   A  88  ASP  HA , Angle CB-CA-HA, observed: 136.191, delta from target: -27.191
   A 131  ILE  HA , Angle C-CA-HA, observed: 81.359, delta from target: 27.641
   A  79  LYS  HA , Angle N-CA-HA, observed: 137.838, delta from target: -27.838
   A 129  ARG  HA , Angle C-CA-HA, observed: 137.402, delta from target: -28.402
   A 131  ILE  HA , Angle CB-CA-HA, observed: 140.160, delta from target: -31.160
   A 131  ILE  HB , Angle CG2-CB-HB, observed: 140.584, delta from target: -31.584
   A 127  ARG  HA , Angle N-CA-HA, observed: 76.336, delta from target: 33.664
   A  22  PRO  HA , Angle C-CA-HA, observed: 74.630, delta from target: 34.370
   A  93  LEU  HA , Angle C-CA-HA, observed: 143.751, delta from target: -34.751
   A  90  SER  HA , Angle C-CA-HA, observed: 143.850, delta from target: -34.850
   A  79  LYS  H  , Angle CA-N-H, observed: 152.165, delta from target: -38.165
   A  76  SER  HA , Angle C-CA-HA, observed: 69.027, delta from target: 39.973
   A 126  VAL  HA , Angle N-CA-HA, observed: 150.505, delta from target: -40.505
   A  79  LYS  H  , Angle C-N-H, observed: 164.841, delta from target: -40.541
   A  74  ASP  HA , Angle C-CA-HA, observed: 67.502, delta from target: 41.498
   A 119  LEU  HA , Angle CB-CA-HA, observed: 151.763, delta from target: -42.763
   A 129  ARG  H  , Angle CA-N-H, observed: 157.015, delta from target: -43.015
   A  77  ILE  HA , Angle N-CA-HA, observed: 153.038, delta from target: -43.038
   A 122  ILE  HB , Angle CG2-CB-HB, observed: 152.981, delta from target: -43.981
   A 129  ARG  H  , Angle C-N-H, observed: 170.013, delta from target: -45.713
   A 128  MET  HA , Angle N-CA-HA, observed: 160.115, delta from target: -50.115
   A 128  MET  HA , Angle CB-CA-HA, observed: 167.787, delta from target: -58.787
   A 128  MET  HA , Angle C-CA-HA, observed: 172.489, delta from target: -62.489

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.975  44.552   2225  Z=48.806
    Angle     :  8.209 105.021   4045  Z= 4.025
    Chirality :  1.940  20.157    176
    Planarity :  0.056   0.443    311
    Dihedral  : 15.800  85.972    754
    Min Nonbonded Distance : 0.453
  
  Molprobity Statistics.
    All-atom Clashscore : 100.36
    Ramachandran Plot:
      Outliers : 11.11 %
      Allowed  : 14.07 %
      Favored  : 74.81 %
    Rotamer:
      Outliers : 12.10 %
      Allowed  :  4.03 %
      Favored  : 83.87 %
    Cbeta Deviations : 27.27 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.78 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.51 (0.63), residues: 135
    helix: -2.82 (0.51), residues: 63
    sheet:  None (None), residues: 0
    loop : -3.23 (0.71), residues: 72
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.037   0.010   HIS A  43 
   PHE   0.101   0.020   PHE A  67 
   TYR   0.986   0.057   TYR A  89 
   ARG   0.179   0.025   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.037   0.010   HIS A  43 
   PHE   0.042   0.014   PHE A  67 
   TYR   0.614   0.046   TYR A  89 
   ARG   0.043   0.009   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 137  HIS
   A 138  HIS

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "  12"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   2.19 %
                favored =  80.29 %
  Rotamer outliers      =  23.39 %
  C-beta deviations     =     0
  Clashscore            =  23.91
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =  11.11 %
                favored =  74.81 %
  Rotamer outliers      =  12.10 %
  C-beta deviations     =    36
  Clashscore            = 100.36
  RMS(bonds)            =   0.9750
  RMS(angles)           =   8.21
  MolProbity score      =   4.09

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  78  ILE  C
   A  79  LYS  N           1.33     1.46    -0.13  1.40e-02  9.14e+01   9.6*sigma
   A  78  ILE  CB
   A  78  ILE  CG1         1.53     1.71    -0.18  2.00e-02  8.32e+01   9.1*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.66    -0.13  2.10e-02  3.90e+01   6.2*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.57    -0.11  1.90e-02  3.32e+01   5.8*sigma
   A  77  ILE  N
   A  77  ILE  CA          1.46     1.54    -0.08  1.90e-02  1.94e+01   4.4*sigma
   A  76  SER  CA
   A  76  SER  C           1.52     1.61    -0.09  2.10e-02  1.73e+01   4.2*sigma
   A  79  LYS  C
   A  80  GLY  N           1.33     1.39    -0.06  1.40e-02  1.68e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.182 (Z=  9.561)
  Mean delta:    0.019 (Z=  0.983)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    90.51    19.99  1.70e+00  1.38e+02  11.8*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40    92.50    17.90  1.70e+00  1.11e+02  10.5*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    81.83    29.17  2.80e+00  1.09e+02  10.4*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   129.57   -19.47  1.90e+00  1.05e+02  10.2*sigma
   A  78  ILE  CG1
   A  78  ILE  CB
   A  78  ILE  CG2       110.70   139.54   -28.84  3.00e+00  9.24e+01   9.6*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60    92.55    19.05  2.00e+00  9.07e+01   9.5*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   138.84   -17.14  1.80e+00  9.07e+01   9.5*sigma
   A  82  THR  CA
   A  82  THR  CB
   A  82  THR  CG2       110.50   125.87   -15.37  1.70e+00  8.17e+01   9.0*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   135.85   -24.85  2.80e+00  7.88e+01   8.9*sigma
   A  78  ILE  CB
   A  78  ILE  CG1
   A  78  ILE  CD1       113.80   132.34   -18.54  2.10e+00  7.80e+01   8.8*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   137.58   -15.88  1.80e+00  7.78e+01   8.8*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   137.13   -15.43  1.80e+00  7.34e+01   8.6*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   107.42    14.28  1.80e+00  6.29e+01   7.9*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   127.43   -13.53  1.80e+00  5.65e+01   7.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.91   -11.01  1.50e+00  5.38e+01   7.3*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  C         111.00   131.11   -20.11  2.80e+00  5.16e+01   7.2*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50    99.38    12.12  1.70e+00  5.08e+01   7.1*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50    99.30    11.20  1.70e+00  4.34e+01   6.6*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   123.52   -11.92  2.00e+00  3.55e+01   6.0*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   125.86   -11.76  2.00e+00  3.46e+01   5.9*sigma
   A  82  THR  N
   A  82  THR  CA
   A  82  THR  C         111.00    94.59    16.41  2.80e+00  3.44e+01   5.9*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  CB        111.50   101.67     9.83  1.70e+00  3.35e+01   5.8*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10    99.30    10.80  1.90e+00  3.23e+01   5.7*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   131.76   -10.06  1.80e+00  3.12e+01   5.6*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   118.00    -5.40  1.00e+00  2.91e+01   5.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.36    -9.66  1.80e+00  2.88e+01   5.4*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N         116.20   106.34     9.86  2.00e+00  2.43e+01   4.9*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   130.50    -8.80  1.80e+00  2.39e+01   4.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.44    -4.84  1.00e+00  2.34e+01   4.8*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   121.18    -9.58  2.00e+00  2.29e+01   4.8*sigma
   A  82  THR  C
   A  82  THR  CA
   A  82  THR  CB        109.10    98.83    10.27  2.20e+00  2.18e+01   4.7*sigma
   A  76  SER  N
   A  76  SER  CA
   A  76  SER  C         111.00   124.02   -13.02  2.80e+00  2.16e+01   4.6*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   106.90     9.30  2.00e+00  2.16e+01   4.6*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   129.75    -8.05  1.80e+00  2.00e+01   4.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   125.12    -8.92  2.00e+00  1.99e+01   4.5*sigma
   A  80  GLY  N
   A  80  GLY  CA
   A  80  GLY  C         113.30   100.60    12.70  2.90e+00  1.92e+01   4.4*sigma
   A  86  ILE  CA
   A  86  ILE  CB
   A  86  ILE  CG1       110.40   117.57    -7.17  1.70e+00  1.78e+01   4.2*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.76e+01   4.2*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   129.26    -7.56  1.80e+00  1.76e+01   4.2*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.78     5.42  1.30e+00  1.74e+01   4.2*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG2       110.50   117.57    -7.07  1.70e+00  1.73e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  C         111.00   122.56   -11.56  2.80e+00  1.70e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:   29.174 (Z= 11.757)
  Mean delta:    3.304 (Z=  1.685)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00    55.36   124.64  5.00e+00  6.21e+02  24.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -68.53  -111.47  5.00e+00  4.97e+02  22.3*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    81.38    98.62  5.00e+00  3.89e+02  19.7*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00    83.83    96.17  5.00e+00  3.70e+02  19.2*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    91.11    88.89  5.00e+00  3.16e+02  17.8*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   -98.49   -81.51  5.00e+00  2.66e+02  16.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -103.49   -76.51  5.00e+00  2.34e+02  15.3*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   116.02    63.98  5.00e+00  1.64e+02  12.8*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -116.59   -63.41  5.00e+00  1.61e+02  12.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   119.29    60.71  5.00e+00  1.47e+02  12.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -122.78   -57.22  5.00e+00  1.31e+02  11.4*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   127.06    52.94  5.00e+00  1.12e+02  10.6*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   129.42    50.58  5.00e+00  1.02e+02  10.1*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   133.31    46.69  5.00e+00  8.72e+01   9.3*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   136.95    43.05  5.00e+00  7.41e+01   8.6*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -136.96   -43.04  5.00e+00  7.41e+01   8.6*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00  -141.54   -38.46  5.00e+00  5.92e+01   7.7*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   144.79    35.21  5.00e+00  4.96e+01   7.0*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   145.61    34.39  5.00e+00  4.73e+01   6.9*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00  -146.80   -33.20  5.00e+00  4.41e+01   6.6*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   148.86    31.14  5.00e+00  3.88e+01   6.2*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00  -151.48   -28.52  5.00e+00  3.25e+01   5.7*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   154.23    25.77  5.00e+00  2.66e+01   5.2*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   155.08    24.92  5.00e+00  2.48e+01   5.0*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   156.09    23.91  5.00e+00  2.29e+01   4.8*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   158.20    21.80  5.00e+00  1.90e+01   4.4*sigma

  Min. delta:    0.132
  Max. delta:  124.644
  Mean delta:   20.589

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.51     6.02  2.00e-01  9.05e+02  30.1*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.88     5.40  2.00e-01  7.29e+02  27.0*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.69     5.33  2.00e-01  7.10e+02  26.7*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.60     5.11  2.00e-01  6.53e+02  25.6*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.53     5.08  2.00e-01  6.45e+02  25.4*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -2.53     5.04  2.00e-01  6.36e+02  25.2*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.44     4.95  2.00e-01  6.11e+02  24.7*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.37     4.81  2.00e-01  5.78e+02  24.0*sigma
   A 131  ILE  CA
   A 131  ILE  N
   A 131  ILE  C
   A 131  ILE  CB          2.43    -0.95     3.39  2.00e-01  2.87e+02  16.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.85     3.28  2.00e-01  2.69e+02  16.4*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     0.18     2.33  2.00e-01  1.36e+02  11.7*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64     1.72     0.93  2.00e-01  2.14e+01   4.6*sigma
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51     1.67     0.84  2.00e-01  1.77e+01   4.2*sigma

  Min. delta:    0.000
  Max. delta:    6.017
  Mean delta:    1.199

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.066       0.127       85.86   6.3*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.090       0.102      161.78   5.1*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.053       0.092       55.23   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.090
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  76  SER  HA , Angle N-CA-HA, observed: 96.730, delta from target: 13.270
   A  82  THR  HB , Angle CA-CB-HB, observed: 95.251, delta from target: 13.749
   A  78  ILE  HA , Angle N-CA-HA, observed: 94.435, delta from target: 15.565
   A  77  ILE  HA , Angle CB-CA-HA, observed: 124.776, delta from target: -15.776
   A  91  TYR  HA , Angle N-CA-HA, observed: 94.197, delta from target: 15.803
   A  88  ASP  HA , Angle N-CA-HA, observed: 93.520, delta from target: 16.480
   A  82  THR  HA , Angle C-CA-HA, observed: 125.625, delta from target: -16.625
   A  51  ILE  HA , Angle CB-CA-HA, observed: 89.710, delta from target: 19.290
   A  51  ILE  HA , Angle C-CA-HA, observed: 87.836, delta from target: 21.164
   A 131  ILE  HA , Angle C-CA-HA, observed: 85.471, delta from target: 23.529
   A  79  LYS  HA , Angle N-CA-HA, observed: 136.480, delta from target: -26.480
   A  78  ILE  HB , Angle CA-CB-HB, observed: 136.311, delta from target: -27.311
   A  78  ILE  HA , Angle CB-CA-HA, observed: 136.700, delta from target: -27.700
   A  77  ILE  HA , Angle C-CA-HA, observed: 80.206, delta from target: 28.794
   A  89  TYR  HA , Angle C-CA-HA, observed: 76.315, delta from target: 32.685
   A  78  ILE  HB , Angle CG2-CB-HB, observed: 71.867, delta from target: 37.133
   A  89  TYR  HA , Angle N-CA-HA, observed: 158.902, delta from target: -48.902
   A  89  TYR  HA , Angle CB-CA-HA, observed: 57.611, delta from target: 51.389

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.182   2242  Z= 0.700
    Angle     :  3.163  51.389   4079  Z= 1.313
    Chirality :  1.199   6.017    176
    Planarity :  0.013   0.099    327
    Dihedral  : 16.394 124.644    769
    Min Nonbonded Distance : 1.357
  
  Molprobity Statistics.
    All-atom Clashscore : 25.25
    Ramachandran Plot:
      Outliers : 10.95 %
      Allowed  : 10.22 %
      Favored  : 78.83 %
    Rotamer:
      Outliers :  8.87 %
      Allowed  :  5.65 %
      Favored  : 85.48 %
    Cbeta Deviations : 12.12 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 16.03 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.91 (0.64), residues: 137
    helix: -2.60 (0.49), residues: 70
    sheet:  None (None), residues: 0
    loop : -2.54 (0.77), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.004   HIS A  43 
   PHE   0.101   0.028   PHE A  15 
   TYR   0.217   0.029   TYR A  89 
   ARG   0.038   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.004   HIS A  43 
   PHE   0.070   0.029   PHE A  15 
   TYR   0.152   0.032   TYR A  89 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =  10.95 %
                favored =  78.83 %
  Rotamer outliers      =   8.87 %
  C-beta deviations     =    16
  Clashscore            =  25.25
  RMS(bonds)            =   0.0135
  RMS(angles)           =   3.16
  MolProbity score      =   3.36

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A LEU  119": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.046 (Z=  2.606)
  Mean delta:    0.013 (Z=  0.682)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        121.70   131.34    -9.64  1.80e+00  2.87e+01   5.4*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   124.90     6.30  1.30e+00  2.35e+01   4.8*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  74  ASP  O         120.80   128.99    -8.19  1.70e+00  2.32e+01   4.8*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   117.23    -4.63  1.00e+00  2.15e+01   4.6*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.19     6.01  1.30e+00  2.14e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.98     4.62  1.00e+00  2.13e+01   4.6*sigma
   A 103  ASP  C
   A 104  VAL  N
   A 104  VAL  CA        121.70   129.99    -8.29  1.80e+00  2.12e+01   4.6*sigma
   A 136  HIS  CA
   A 136  HIS  CB
   A 136  HIS  CG        113.80   118.29    -4.49  1.00e+00  2.02e+01   4.5*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   121.33    -7.43  1.80e+00  1.71e+01   4.1*sigma

  Min. delta:    0.004 (Z=  0.002)
  Max. delta:   10.785 (Z=  5.356)
  Mean delta:    2.152 (Z=  1.168)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   -73.03  -106.97  5.00e+00  4.58e+02  21.4*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -121.77   -58.23  5.00e+00  1.36e+02  11.6*sigma
   A  71  ILE  CA
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        180.00  -130.06   -49.94  5.00e+00  9.98e+01  10.0*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   157.60    22.40  5.00e+00  2.01e+01   4.5*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00   158.59    21.41  5.00e+00  1.83e+01   4.3*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   159.36    20.64  5.00e+00  1.70e+01   4.1*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   159.64    20.36  5.00e+00  1.66e+01   4.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -159.88   -20.12  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.006
  Max. delta:  106.971
  Mean delta:   16.708

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  72  ASN  CA
   A  72  ASN  N
   A  72  ASN  C
   A  72  ASN  CB          2.51    -1.75     4.26  2.00e-01  4.53e+02  21.3*sigma

  Min. delta:    0.000
  Max. delta:    4.257
  Mean delta:    0.337

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  ND1
   A 136  HIS  CD2
   A 136  HIS  CE1
   A 136  HIS  NE2           0.096       0.135      138.06   6.8*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.076       0.132      115.09   6.6*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.064       0.106       82.28   5.3*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.051       0.103       51.51   5.2*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.078       0.095      121.79   4.8*sigma

  Min. delta:    0.000
  Max. delta:    0.103
  Mean delta:    0.021

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  74  ASP  HA , Angle N-CA-HA, observed: 97.000, delta from target: 13.000
   A  72  ASN  HA , Angle C-CA-HA, observed: 93.424, delta from target: 15.576

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.046   2242  Z= 0.485
    Angle     :  1.940  15.576   4079  Z= 0.860
    Chirality :  0.337   4.257    176
    Planarity :  0.016   0.095    327
    Dihedral  : 14.353 106.971    769
    Min Nonbonded Distance : 1.759
  
  Molprobity Statistics.
    All-atom Clashscore : 9.92
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.11 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  8.06 %
      Favored  : 87.10 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.61 (0.68), residues: 137
    helix: -1.68 (0.45), residues: 65
    sheet:  None (None), residues: 0
    loop : -0.29 (0.84), residues: 72
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.030   0.008   HIS A 134 
   PHE   0.101   0.020   PHE A  67 
   TYR   0.193   0.039   TYR A 111 
   ARG   0.084   0.021   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.030   0.008   HIS A 134 
   PHE   0.070   0.019   PHE A  67 
   TYR   0.154   0.040   TYR A 111 
   ARG   0.007   0.003   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   5" pdb=" CB  ILE A  51 "
        model="   5" pdb=" CB  ILE A  78 "
        model="   5" pdb=" CB  LYS A  79 "
        model="   5" pdb=" CB  ASP A  88 "
        model="   5" pdb=" CB  TYR A  89 "
        model="   5" pdb=" CB  TYR A  91 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Ramachandran outliers =   2.19 %
                favored =  92.70 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     1
  Clashscore            =   9.92
  RMS(bonds)            =   0.0095
  RMS(angles)           =   1.94
  MolProbity score      =   2.50

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   4" pdb=" CB  ILE A  51 "
        model="   4" pdb=" CB  ILE A  77 "
        model="   4" pdb=" CB  LYS A  79 "
        model="   4" pdb=" CB  TYR A  89 "
        model="   4" pdb=" CB  SER A  90 "
        model="   4" pdb=" CB  SER A  97 "
        model="   4" pdb=" CB  LEU A 119 "
        model="   4" pdb=" CB  GLU A 123 "
        model="   4" pdb=" CB  LYS A 125 "
        model="   4" pdb=" CB  VAL A 126 "
  Number of C-beta restraints generated:  244

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 63
        1.23 -     1.43: 411
        1.43 -     1.62: 658
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   5" pdb=" N   GLY A  80 "
       model="   5" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.557 -0.106 1.60e-02 3.91e+03 4.38e+01
  bond model="   5" pdb=" N   TYR A  91 "
       model="   5" pdb=" CA  TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.458  1.519 -0.061 1.90e-02 2.77e+03 1.04e+01
  bond model="   5" pdb=" CA  SER A  97 "
       model="   5" pdb=" CB  SER A  97 "
    ideal  model  delta    sigma   weight residual
    1.530  1.473  0.057 2.00e-02 2.50e+03 8.13e+00
  bond model="   5" pdb=" CD2 HIS A 137 "
       model="   5" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.82e+00
  bond model="   5" pdb=" CD2 HIS A 139 "
       model="   5" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.66e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       87.13 -    97.80: 6
       97.80 -   108.48: 677
      108.48 -   119.15: 2498
      119.15 -   129.83: 890
      129.83 -   140.50: 8
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   5" pdb=" C   SER A  90 "
        model="   5" pdb=" N   TYR A  91 "
        model="   5" pdb=" CA  TYR A  91 "
      ideal   model   delta    sigma   weight residual
     121.70  140.50  -18.80 1.80e+00 3.09e-01 1.09e+02
  angle model="   5" pdb=" C   ASP A  88 "
        model="   5" pdb=" N   TYR A  89 "
        model="   5" pdb=" CA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     121.70  140.02  -18.32 1.80e+00 3.09e-01 1.04e+02
  angle model="   5" pdb=" C   TYR A  89 "
        model="   5" pdb=" CA  TYR A  89 "
        model="   5" pdb=" CB  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     110.10  126.64  -16.54 1.90e+00 2.77e-01 7.58e+01
  angle model="   5" pdb=" CB  SER A  90 "
        model="   5" pdb=" CA  SER A  90 "
        model="   5" pdb=" HA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     109.00   87.13   21.87 3.00e+00 1.11e-01 5.31e+01
  angle model="   5" pdb=" C   TYR A  89 "
        model="   5" pdb=" CA  TYR A  89 "
        model="   5" pdb=" HA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.00   88.84   20.16 3.00e+00 1.11e-01 4.52e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.95: 897
       13.95 -    27.90: 86
       27.90 -    41.85: 22
       41.85 -    55.80: 12
       55.80 -    69.75: 4
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   5" pdb=" CA  TYR A  91 "
           model="   5" pdb=" C   TYR A  91 "
           model="   5" pdb=" N   THR A  92 "
           model="   5" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -110.25  -69.75     0      5.00e+00 4.00e-02 1.95e+02
  dihedral model="   5" pdb=" CA  ILE A  51 "
           model="   5" pdb=" C   ILE A  51 "
           model="   5" pdb=" N   PRO A  52 "
           model="   5" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -110.84  -69.16     0      5.00e+00 4.00e-02 1.91e+02
  dihedral model="   5" pdb=" CA  LYS A  79 "
           model="   5" pdb=" C   LYS A  79 "
           model="   5" pdb=" N   GLY A  80 "
           model="   5" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  128.01   51.99     0      5.00e+00 4.00e-02 1.08e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.002: 169
       1.002 -    2.004: 1
       2.004 -    3.006: 0
       3.006 -    4.008: 1
       4.008 -    5.010: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   5" pdb=" CA  LYS A  79 "
            model="   5" pdb=" N   LYS A  79 "
            model="   5" pdb=" C   LYS A  79 "
            model="   5" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.50    5.01 2.00e-01 2.50e+01 6.27e+02
  chirality model="   5" pdb=" CA  ASP A  88 "
            model="   5" pdb=" N   ASP A  88 "
            model="   5" pdb=" C   ASP A  88 "
            model="   5" pdb=" CB  ASP A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.22    4.73 2.00e-01 2.50e+01 5.59e+02
  chirality model="   5" pdb=" CA  TYR A  89 "
            model="   5" pdb=" N   TYR A  89 "
            model="   5" pdb=" C   TYR A  89 "
            model="   5" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.92    4.43 2.00e-01 2.50e+01 4.91e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  91 "   -0.207 2.00e-02 2.50e+03   9.25e-02 2.57e+02
        model="   5" pdb=" CG  TYR A  91 "   -0.022 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  91 "    0.037 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  91 "    0.047 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  91 "    0.030 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  91 "    0.020 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  91 "   -0.040 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  91 "   -0.166 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  91 "    0.081 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  91 "    0.109 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  91 "    0.071 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  91 "    0.042 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  50 "    0.116 2.00e-02 2.50e+03   4.50e-02 6.08e+01
        model="   5" pdb=" CG  TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  50 "    0.068 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  50 "   -0.041 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  50 "   -0.043 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   5" pdb=" CB  TYR A  12 "   -0.085 2.00e-02 2.50e+03   4.01e-02 4.82e+01
        model="   5" pdb=" CG  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   5" pdb=" CD1 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   5" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   5" pdb=" CE1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   5" pdb=" CE2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   5" pdb=" CZ  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   5" pdb=" OH  TYR A  12 "   -0.087 2.00e-02 2.50e+03
        model="   5" pdb=" HD1 TYR A  12 "    0.039 2.00e-02 2.50e+03
        model="   5" pdb=" HD2 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   5" pdb=" HE1 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   5" pdb=" HE2 TYR A  12 "    0.039 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.29: 370
        2.29 -     2.87: 5164
        2.87 -     3.45: 5791
        3.45 -     4.02: 7588
        4.02 -     4.60: 11311
  Nonbonded interactions: 30224
  Sorted by model distance:
  nonbonded model="   5" pdb=" H   LYS A  79 "
            model="   5" pdb=" HB  THR A  92 "
     model   vdw
     1.717 2.270
  nonbonded model="   5" pdb=" O   LEU A  61 "
            model="   5" pdb=" HG  SER A  65 "
     model   vdw
     1.812 1.850
  nonbonded model="   5" pdb=" HA  SER A  97 "
            model="   5" pdb=" H   SER A  98 "
     model   vdw
     1.824 2.270
  nonbonded model="   5" pdb=" HA  SER A  90 "
            model="   5" pdb=" HB3 SER A  90 "
     model   vdw
     1.834 1.952
  nonbonded model="   5" pdb=" O   ASP A   7 "
            model="   5" pdb=" HG  SER A  11 "
     model   vdw
     1.835 1.850
  ... (remaining 30219 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.023, 42.507, 51.253, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.850)
  Mean delta:    0.014 (Z=  0.710)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma
   A  41  VAL  CG1
   A  41  VAL  CB
   A  41  VAL  CG2       110.80   101.78     9.02  2.20e+00  1.68e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.54     4.06  1.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    9.023 (Z=  4.169)
  Mean delta:    1.920 (Z=  1.041)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A   1  MET  CA
   A   1  MET  C
   A   2  LEU  N
   A   2  LEU  CA        180.00  -141.67   -38.33  5.00e+00  5.88e+01   7.7*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   154.45    25.55  5.00e+00  2.61e+01   5.1*sigma

  Min. delta:    0.013
  Max. delta:   87.126
  Mean delta:   18.661

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.245
  Mean delta:    0.089

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.058       0.114       66.79   5.7*sigma

  Min. delta:    0.000
  Max. delta:    0.075
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.040   2242  Z= 0.506
    Angle     :  1.769   9.203   4079  Z= 0.776
    Chirality :  0.089   0.245    176
    Planarity :  0.012   0.063    327
    Dihedral  : 15.454  87.126    769
    Min Nonbonded Distance : 1.690
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  8.87 %
      Allowed  :  5.65 %
      Favored  : 85.48 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.41 (0.70), residues: 137
    helix: -0.95 (0.50), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.67 (0.95), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.035   0.006   HIS A  43 
   PHE   0.073   0.016   PHE A  45 
   TYR   0.144   0.019   TYR A 111 
   ARG   0.063   0.014   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.035   0.006   HIS A  43 
   PHE   0.041   0.013   PHE A  45 
   TYR   0.114   0.022   TYR A 111 
   ARG   0.009   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 53
        1.23 -     1.43: 423
        1.43 -     1.62: 653
        1.62 -     1.82: 7
  Bond restraints: 2242
  Sorted by residual:
  bond model="   4" pdb=" N   LYS A 125 "
       model="   4" pdb=" CA  LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.656 -0.198 1.90e-02 2.77e+03 1.09e+02
  bond model="   4" pdb=" C   ALA A 124 "
       model="   4" pdb=" N   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.20e+01
  bond model="   4" pdb=" CA  ALA A 124 "
       model="   4" pdb=" C   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.525  1.645 -0.120 2.10e-02 2.27e+03 3.26e+01
  bond model="   4" pdb=" C   VAL A 126 "
       model="   4" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.253  0.076 1.40e-02 5.10e+03 2.91e+01
  bond model="   4" pdb=" CA  GLU A 123 "
       model="   4" pdb=" CB  GLU A 123 "
    ideal  model  delta    sigma   weight residual
    1.530  1.628 -0.098 2.00e-02 2.50e+03 2.39e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       74.42 -    89.31: 5
       89.31 -   104.21: 94
      104.21 -   119.11: 3076
      119.11 -   134.01: 900
      134.01 -   148.91: 4
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   4" pdb=" C   ALA A 124 "
        model="   4" pdb=" N   LYS A 125 "
        model="   4" pdb=" CA  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     121.70  148.91  -27.21 1.80e+00 3.09e-01 2.28e+02
  angle model="   4" pdb=" CA  VAL A 126 "
        model="   4" pdb=" CB  VAL A 126 "
        model="   4" pdb=" CG2 VAL A 126 "
      ideal   model   delta    sigma   weight residual
     110.40  134.60  -24.20 1.70e+00 3.46e-01 2.03e+02
  angle model="   4" pdb=" C   ARG A 129 "
        model="   4" pdb=" CA  ARG A 129 "
        model="   4" pdb=" CB  ARG A 129 "
      ideal   model   delta    sigma   weight residual
     110.10  135.19  -25.09 1.90e+00 2.77e-01 1.74e+02
  angle model="   4" pdb=" C   LYS A 125 "
        model="   4" pdb=" N   VAL A 126 "
        model="   4" pdb=" CA  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     121.70   98.43   23.27 1.80e+00 3.09e-01 1.67e+02
  angle model="   4" pdb=" C   LYS A 125 "
        model="   4" pdb=" CA  LYS A 125 "
        model="   4" pdb=" HA  LYS A 125 "
      ideal   model   delta    sigma   weight residual
     109.00   74.42   34.58 3.00e+00 1.11e-01 1.33e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.56: 938
       24.56 -    49.12: 54
       49.12 -    73.69: 13
       73.69 -    98.25: 7
       98.25 -   122.81: 1
  Dihedral angle restraints: 1013
    sinusoidal: 562
      harmonic: 451
  Sorted by residual:
  dihedral model="   4" pdb=" CA  GLU A 123 "
           model="   4" pdb=" C   GLU A 123 "
           model="   4" pdb=" N   ALA A 124 "
           model="   4" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   57.19  122.81     0      5.00e+00 4.00e-02 6.03e+02
  dihedral model="   4" pdb=" CA  VAL A 126 "
           model="   4" pdb=" C   VAL A 126 "
           model="   4" pdb=" N   ARG A 127 "
           model="   4" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   92.81   87.19     0      5.00e+00 4.00e-02 3.04e+02
  dihedral model="   4" pdb=" CA  ASP A  74 "
           model="   4" pdb=" C   ASP A  74 "
           model="   4" pdb=" N   GLU A  75 "
           model="   4" pdb=" CA  GLU A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   94.12   85.88     0      5.00e+00 4.00e-02 2.95e+02
  ... (remaining 1010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.009: 164
       1.009 -    2.017: 1
       2.017 -    3.025: 0
       3.025 -    4.033: 2
       4.033 -    5.042: 9
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   4" pdb=" CA  TYR A  89 "
            model="   4" pdb=" N   TYR A  89 "
            model="   4" pdb=" C   TYR A  89 "
            model="   4" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.53    5.04 2.00e-01 2.50e+01 6.35e+02
  chirality model="   4" pdb=" CB  ILE A  77 "
            model="   4" pdb=" CA  ILE A  77 "
            model="   4" pdb=" CG1 ILE A  77 "
            model="   4" pdb=" CG2 ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.25    4.90 2.00e-01 2.50e+01 5.99e+02
  chirality model="   4" pdb=" CA  ILE A  77 "
            model="   4" pdb=" N   ILE A  77 "
            model="   4" pdb=" C   ILE A  77 "
            model="   4" pdb=" CB  ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43   -2.41    4.84 2.00e-01 2.50e+01 5.86e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  PHE A  67 "   -0.066 2.00e-02 2.50e+03   6.83e-02 1.40e+02
        model="   4" pdb=" CG  PHE A  67 "   -0.026 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 PHE A  67 "    0.040 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 PHE A  67 "   -0.017 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 PHE A  67 "   -0.014 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 PHE A  67 "    0.043 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  PHE A  67 "   -0.033 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 PHE A  67 "    0.121 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 PHE A  67 "   -0.051 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 PHE A  67 "   -0.038 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 PHE A  67 "    0.135 2.00e-02 2.50e+03
        model="   4" pdb=" HZ  PHE A  67 "   -0.095 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A  89 "    0.109 2.00e-02 2.50e+03   6.39e-02 1.22e+02
        model="   4" pdb=" CG  TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A  89 "   -0.052 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A  89 "    0.026 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A  89 "   -0.025 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A  89 "    0.016 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A  89 "    0.034 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A  89 "   -0.141 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A  89 "    0.085 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A  89 "   -0.066 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   4" pdb=" CB  TYR A 111 "    0.123 2.00e-02 2.50e+03   5.17e-02 8.03e+01
        model="   4" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   4" pdb=" CD1 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   4" pdb=" CD2 TYR A 111 "   -0.029 2.00e-02 2.50e+03
        model="   4" pdb=" CE1 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   4" pdb=" CE2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   4" pdb=" CZ  TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   4" pdb=" OH  TYR A 111 "    0.099 2.00e-02 2.50e+03
        model="   4" pdb=" HD1 TYR A 111 "   -0.033 2.00e-02 2.50e+03
        model="   4" pdb=" HD2 TYR A 111 "   -0.048 2.00e-02 2.50e+03
        model="   4" pdb=" HE1 TYR A 111 "   -0.034 2.00e-02 2.50e+03
        model="   4" pdb=" HE2 TYR A 111 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.41 -     2.05: 71
        2.05 -     2.69: 3348
        2.69 -     3.32: 6892
        3.32 -     3.96: 8329
        3.96 -     4.60: 12490
  Nonbonded interactions: 31130
  Sorted by model distance:
  nonbonded model="   4" pdb="HG22 ILE A 131 "
            model="   4" pdb=" H   LEU A 132 "
     model   vdw
     1.412 2.270
  nonbonded model="   4" pdb=" HA  VAL A 126 "
            model="   4" pdb=" H   MET A 128 "
     model   vdw
     1.447 2.270
  nonbonded model="   4" pdb=" HB2 ARG A 129 "
            model="   4" pdb=" H   GLU A 133 "
     model   vdw
     1.704 2.270
  nonbonded model="   4" pdb="HG23 THR A  92 "
            model="   4" pdb=" H   LEU A  99 "
     model   vdw
     1.744 2.270
  nonbonded model="   4" pdb=" HA  LEU A 119 "
            model="   4" pdb=" H   GLU A 120 "
     model   vdw
     1.760 2.270
  ... (remaining 31125 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   2"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   0.73 %
                favored =  94.16 %
  Rotamer outliers      =   8.87 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0097
  RMS(angles)           =   1.77
  MolProbity score      =   2.43

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.83, per 1000 atoms: 0.37
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.155, 56.407, 47.011, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 0.65, per 1000 atoms: 0.29
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.626, 51.236, 56.738, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.562)
  Mean delta:    0.001 (Z=  0.063)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.605 (Z=  1.344)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   84.597
  Mean delta:   22.826

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.094
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.046
    Angle     :  0.979   4.826   4077  Z= 0.341
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 17.984  84.597    768
    Min Nonbonded Distance : 1.527
  
  Molprobity Statistics.
    All-atom Clashscore : 22.10
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  : 21.17 %
      Favored  : 75.18 %
    Rotamer:
      Outliers : 18.55 %
      Allowed  : 27.42 %
      Favored  : 54.03 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.26 (0.48), residues: 137
    helix: -4.01 (0.36), residues: 65
    sheet:  None (None), residues: 0
    loop : -4.45 (0.57), residues: 72
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 136 
   PHE   0.002   0.001   PHE A  15 
   TYR   0.003   0.001   TYR A 105 
   ARG   0.001   0.000   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 136 
   PHE   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A 105 
   ARG   0.001   0.000   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 136  HIS

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A VAL  126": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   3.65 %
                favored =  75.18 %
  Rotamer outliers      =  18.55 %
  C-beta deviations     =     0
  Clashscore            =  22.10
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.59

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A LEU   39": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.64    -0.12  2.10e-02  3.04e+01   5.5*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.56    -0.10  1.90e-02  2.89e+01   5.4*sigma
   A  88  ASP  C
   A  89  TYR  N           1.33     1.40    -0.07  1.40e-02  2.25e+01   4.7*sigma

  Min. delta:    0.000 (Z=  0.003)
  Max. delta:    0.116 (Z=  5.511)
  Mean delta:    0.015 (Z=  0.769)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   140.19   -18.49  1.80e+00  1.06e+02  10.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.28   -11.38  1.50e+00  5.75e+01   7.6*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   122.70   -12.20  1.70e+00  5.15e+01   7.2*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   134.51   -12.81  1.80e+00  5.06e+01   7.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    91.52    19.48  2.80e+00  4.84e+01   7.0*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   122.83   -12.73  1.90e+00  4.49e+01   6.7*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   133.58   -11.88  1.80e+00  4.35e+01   6.6*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   126.71   -12.61  2.00e+00  3.98e+01   6.3*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   120.80   -10.30  1.70e+00  3.67e+01   6.1*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   128.00   -11.80  2.00e+00  3.48e+01   5.9*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.98   -10.28  1.80e+00  3.26e+01   5.7*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.77    -5.17  1.00e+00  2.67e+01   5.2*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.90   -10.30  2.00e+00  2.65e+01   5.1*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   130.88    -9.18  1.80e+00  2.60e+01   5.1*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   120.78    -9.18  2.00e+00  2.11e+01   4.6*sigma
   A  99  LEU  N
   A  99  LEU  CA
   A  99  LEU  CB        110.50   102.75     7.75  1.70e+00  2.08e+01   4.6*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   129.88    -8.18  1.80e+00  2.06e+01   4.5*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   107.31     8.89  2.00e+00  1.97e+01   4.4*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   102.97     7.53  1.70e+00  1.96e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.51     5.69  1.30e+00  1.92e+01   4.4*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   118.18    -4.38  1.00e+00  1.91e+01   4.4*sigma
   A  88  ASP  O
   A  88  ASP  C
   A  89  TYR  N         123.00   116.04     6.96  1.60e+00  1.89e+01   4.3*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD1       110.70   123.58   -12.88  3.00e+00  1.84e+01   4.3*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30   100.93     8.37  2.00e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   129.16    -7.46  1.80e+00  1.72e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.96     6.84  1.70e+00  1.62e+01   4.0*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   117.33    -6.83  1.70e+00  1.62e+01   4.0*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.60     4.00  1.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:   19.485 (Z= 10.272)
  Mean delta:    2.583 (Z=  1.384)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -53.61  -126.39  5.00e+00  6.39e+02  25.3*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00    94.33    85.67  5.00e+00  2.94e+02  17.1*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00    95.22    84.78  5.00e+00  2.88e+02  17.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   109.55    70.45  5.00e+00  1.99e+02  14.1*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   110.17    69.83  5.00e+00  1.95e+02  14.0*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   129.60    50.40  5.00e+00  1.02e+02  10.1*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   138.12    41.88  5.00e+00  7.02e+01   8.4*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   142.79    37.21  5.00e+00  5.54e+01   7.4*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -145.00   -35.00  5.00e+00  4.90e+01   7.0*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   148.90    31.10  5.00e+00  3.87e+01   6.2*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00   150.41    29.59  5.00e+00  3.50e+01   5.9*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -150.91   -29.09  5.00e+00  3.38e+01   5.8*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   154.24    25.76  5.00e+00  2.65e+01   5.2*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   154.40    25.60  5.00e+00  2.62e+01   5.1*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   155.11    24.89  5.00e+00  2.48e+01   5.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   157.55    22.45  5.00e+00  2.02e+01   4.5*sigma

  Min. delta:    0.009
  Max. delta:  126.393
  Mean delta:   17.713

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.99     5.63  2.00e-01  7.93e+02  28.2*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.79     5.30  2.00e-01  7.01e+02  26.5*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.52     5.03  2.00e-01  6.33e+02  25.2*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.33     4.84  2.00e-01  5.85e+02  24.2*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.31     4.83  2.00e-01  5.84e+02  24.2*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.69     4.12  2.00e-01  4.25e+02  20.6*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.94     3.37  2.00e-01  2.84e+02  16.8*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     1.55     0.96  2.00e-01  2.32e+01   4.8*sigma

  Min. delta:    0.000
  Max. delta:    5.632
  Mean delta:    0.965

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O
   A  78  ILE  N             0.064       0.111       41.28   5.6*sigma

  Min. delta:    0.000
  Max. delta:    0.092
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  81  TYR  HA , Angle C-CA-HA, observed: 94.393, delta from target: 14.607
   A  79  LYS  HA , Angle C-CA-HA, observed: 123.916, delta from target: -14.916
   A  79  LYS  HA , Angle CB-CA-HA, observed: 93.681, delta from target: 15.319
   A  78  ILE  HA , Angle CB-CA-HA, observed: 92.681, delta from target: 16.319
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.015, delta from target: 16.985
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.493, delta from target: 17.507

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.116   2242  Z= 0.547
    Angle     :  2.287  19.485   4079  Z= 1.012
    Chirality :  0.965   5.632    176
    Planarity :  0.012   0.092    327
    Dihedral  : 14.592 126.393    769
    Min Nonbonded Distance : 1.487
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  8.76 %
      Allowed  :  7.30 %
      Favored  : 83.94 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  3.23 %
      Favored  : 90.32 %
    Cbeta Deviations :  9.09 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 7.63 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.51 (0.63), residues: 137
    helix: -2.03 (0.46), residues: 80
    sheet:  None (None), residues: 0
    loop : -2.65 (0.85), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 139 
   PHE   0.030   0.011   PHE A  45 
   TYR   0.110   0.020   TYR A  12 
   ARG   0.030   0.006   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A 139 
   PHE   0.023   0.009   PHE A  45 
   TYR   0.090   0.022   TYR A  12 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  98  SER  N
   A  98  SER  CA          1.46     1.38     0.08  1.90e-02  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.078 (Z=  4.085)
  Mean delta:    0.015 (Z=  0.781)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   134.46   -24.36  1.90e+00  1.64e+02  12.8*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   137.73   -16.03  1.80e+00  7.94e+01   8.9*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10   126.55   -16.45  1.90e+00  7.49e+01   8.7*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10    94.57    15.53  1.90e+00  6.68e+01   8.2*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    95.86    14.24  1.90e+00  5.62e+01   7.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.04   -11.14  1.50e+00  5.52e+01   7.4*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   134.64   -12.94  1.80e+00  5.17e+01   7.2*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   134.42   -12.72  1.80e+00  5.00e+01   7.1*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   123.19   -13.09  1.90e+00  4.75e+01   6.9*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   121.06   -10.56  1.70e+00  3.86e+01   6.2*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.43   -10.73  1.80e+00  3.56e+01   6.0*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   104.42    11.78  2.00e+00  3.47e+01   5.9*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   124.94   -10.84  2.00e+00  2.94e+01   5.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.35    -9.65  1.80e+00  2.88e+01   5.4*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50   102.64     8.86  1.70e+00  2.72e+01   5.2*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.88   -10.28  2.00e+00  2.64e+01   5.1*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   123.04   -11.74  2.30e+00  2.60e+01   5.1*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.23    -4.63  1.00e+00  2.14e+01   4.6*sigma
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        121.70   129.99    -8.29  1.80e+00  2.12e+01   4.6*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N         116.20   107.15     9.05  2.00e+00  2.05e+01   4.5*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   116.92    -4.32  1.00e+00  1.87e+01   4.3*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   116.14     6.86  1.60e+00  1.84e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.73     5.47  1.30e+00  1.77e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   103.57     6.93  1.70e+00  1.66e+01   4.1*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   116.49     6.51  1.60e+00  1.65e+01   4.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   124.25    -8.05  2.00e+00  1.62e+01   4.0*sigma
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        121.70   128.92    -7.22  1.80e+00  1.61e+01   4.0*sigma

  Min. delta:    0.015 (Z=  0.005)
  Max. delta:   24.360 (Z= 12.821)
  Mean delta:    2.611 (Z=  1.415)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -54.28  -125.72  5.00e+00  6.32e+02  25.1*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   -64.87  -115.13  5.00e+00  5.30e+02  23.0*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   -91.66   -88.34  5.00e+00  3.12e+02  17.7*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   115.06    64.94  5.00e+00  1.69e+02  13.0*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   124.31    55.69  5.00e+00  1.24e+02  11.1*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -124.91   -55.09  5.00e+00  1.21e+02  11.0*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   133.11    46.89  5.00e+00  8.79e+01   9.4*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   135.03    44.97  5.00e+00  8.09e+01   9.0*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   141.32    38.68  5.00e+00  5.98e+01   7.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -142.73   -37.27  5.00e+00  5.56e+01   7.5*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   149.85    30.15  5.00e+00  3.64e+01   6.0*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -155.31   -24.69  5.00e+00  2.44e+01   4.9*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA          0.00   -22.93    22.93  5.00e+00  2.10e+01   4.6*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -157.88   -22.12  5.00e+00  1.96e+01   4.4*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   158.61    21.39  5.00e+00  1.83e+01   4.3*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   159.69    20.31  5.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.002
  Max. delta:  125.724
  Mean delta:   17.574

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.40     5.91  2.00e-01  8.72e+02  29.5*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.62     5.26  2.00e-01  6.92e+02  26.3*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.49     5.00  2.00e-01  6.25e+02  25.0*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.39     4.90  2.00e-01  6.01e+02  24.5*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.39     4.82  2.00e-01  5.81e+02  24.1*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.28     4.79  2.00e-01  5.74e+02  23.9*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.48     3.99  2.00e-01  3.97e+02  19.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.93     3.36  2.00e-01  2.83e+02  16.8*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51     1.56     0.95  2.00e-01  2.28e+01   4.8*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51     1.60     0.91  2.00e-01  2.09e+01   4.6*sigma

  Min. delta:    0.003
  Max. delta:    5.907
  Mean delta:    1.039

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.111       0.200      244.35  10.0*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.098       0.189      193.12   9.5*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  93  LEU  O
   A  94  GLY  N             0.060       0.104       36.08   5.2*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.050       0.088       49.57   4.4*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O
   A  78  ILE  N             0.049       0.085       24.29   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.111
  Mean delta:    0.019

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  74  ASP  HA , Angle C-CA-HA, observed: 96.490, delta from target: 12.510
   A  74  ASP  HA , Angle CB-CA-HA, observed: 95.318, delta from target: 13.682
   A  89  TYR  HA , Angle C-CA-HA, observed: 94.959, delta from target: 14.041
   A  79  LYS  HA , Angle C-CA-HA, observed: 123.124, delta from target: -14.124
   A  93  LEU  HA , Angle CB-CA-HA, observed: 123.759, delta from target: -14.759
   A  81  TYR  HA , Angle C-CA-HA, observed: 93.575, delta from target: 15.425
   A  51  ILE  HA , Angle CB-CA-HA, observed: 91.960, delta from target: 17.040
   A  51  ILE  HA , Angle C-CA-HA, observed: 91.521, delta from target: 17.479
   A  89  TYR  HA , Angle N-CA-HA, observed: 129.429, delta from target: -19.429
   A  90  SER  HA , Angle CB-CA-HA, observed: 86.310, delta from target: 22.690
   A  89  TYR  HA , Angle CB-CA-HA, observed: 82.309, delta from target: 26.691

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.078   2242  Z= 0.556
    Angle     :  2.342  26.691   4079  Z= 1.039
    Chirality :  1.039   5.907    176
    Planarity :  0.014   0.107    327
    Dihedral  : 14.562 125.724    769
    Min Nonbonded Distance : 1.462
  
  Molprobity Statistics.
    All-atom Clashscore : 14.43
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  :  5.84 %
      Favored  : 86.13 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  1.61 %
      Favored  : 93.55 %
    Cbeta Deviations :  9.85 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 8.40 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.87 (0.70), residues: 137
    helix: -2.04 (0.45), residues: 79
    sheet:  None (None), residues: 0
    loop : -1.49 (1.00), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A 135 
   PHE   0.100   0.017   PHE A  15 
   TYR   0.250   0.034   TYR A  91 
   ARG   0.042   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A 135 
   PHE   0.069   0.018   PHE A  15 
   TYR   0.200   0.040   TYR A  91 
   ARG   0.004   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   8.76 %
                favored =  83.94 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    12
  Clashscore            =   7.66
  RMS(bonds)            =   0.0105
  RMS(angles)           =   2.29
  MolProbity score      =   2.71

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Ramachandran outliers =   8.03 %
                favored =  86.13 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =    13
  Clashscore            =  14.43
  RMS(bonds)            =   0.0107
  RMS(angles)           =   2.34
  MolProbity score      =   2.82

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 87
        1.23 -     1.43: 385
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  10" pdb=" CZ  ARG A  21 "
       model="  10" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 8.78e+00
  bond model="  10" pdb=" CD2 HIS A 136 "
       model="  10" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.63e+00
  bond model="  10" pdb=" CD2 HIS A 138 "
       model="  10" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.61e+00
  bond model="  10" pdb=" CD2 HIS A 139 "
       model="  10" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.40e+00
  bond model="  10" pdb=" CZ  ARG A  58 "
       model="  10" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.40e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.91 -   104.83: 49
      104.83 -   110.76: 2235
      110.76 -   116.68: 738
      116.68 -   122.60: 749
      122.60 -   128.53: 308
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  10" pdb=" OE1 GLN A  28 "
        model="  10" pdb=" CD  GLN A  28 "
        model="  10" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.11    4.49 1.00e+00 1.00e+00 2.01e+01
  angle model="  10" pdb=" OE1 GLN A  66 "
        model="  10" pdb=" CD  GLN A  66 "
        model="  10" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.26    4.34 1.00e+00 1.00e+00 1.89e+01
  angle model="  10" pdb=" CA  PRO A 117 "
        model="  10" pdb=" N   PRO A 117 "
        model="  10" pdb=" CD  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     112.00  106.52    5.48 1.40e+00 5.10e-01 1.53e+01
  angle model="  10" pdb=" CB  HIS A  43 "
        model="  10" pdb=" CG  HIS A  43 "
        model="  10" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.35    4.85 1.30e+00 5.92e-01 1.39e+01
  angle model="  10" pdb=" CA  ASP A 118 "
        model="  10" pdb=" CB  ASP A 118 "
        model="  10" pdb=" CG  ASP A 118 "
      ideal   model   delta    sigma   weight residual
     112.60  116.20   -3.60 1.00e+00 1.00e+00 1.30e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.94: 896
       13.94 -    27.87: 91
       27.87 -    41.81: 25
       41.81 -    55.74: 11
       55.74 -    69.68: 10
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="  10" pdb=" CA  PRO A 114 "
           model="  10" pdb=" C   PRO A 114 "
           model="  10" pdb=" N   ALA A 115 "
           model="  10" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.67   26.33     0      5.00e+00 4.00e-02 2.77e+01
  dihedral model="  10" pdb=" CA  ILE A  51 "
           model="  10" pdb=" C   ILE A  51 "
           model="  10" pdb=" N   PRO A  52 "
           model="  10" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -24.44   24.44     0      5.00e+00 4.00e-02 2.39e+01
  dihedral model="  10" pdb=" CA  PRO A 117 "
           model="  10" pdb=" C   PRO A 117 "
           model="  10" pdb=" N   ASP A 118 "
           model="  10" pdb=" CA  ASP A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.94  -21.06     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 76
       0.043 -    0.086: 42
       0.086 -    0.129: 27
       0.129 -    0.173: 26
       0.173 -    0.216: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  10" pdb=" CG  LEU A  64 "
            model="  10" pdb=" CB  LEU A  64 "
            model="  10" pdb=" CD1 LEU A  64 "
            model="  10" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.81    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality model="  10" pdb=" CA  VAL A 112 "
            model="  10" pdb=" N   VAL A 112 "
            model="  10" pdb=" C   VAL A 112 "
            model="  10" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality model="  10" pdb=" CA  TYR A  50 "
            model="  10" pdb=" N   TYR A  50 "
            model="  10" pdb=" C   TYR A  50 "
            model="  10" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.04e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  50 "    0.252 2.00e-02 2.50e+03   1.15e-01 4.00e+02
        model="  10" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  50 "   -0.048 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  50 "   -0.051 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  50 "   -0.043 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  50 "   -0.039 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  50 "    0.240 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  50 "   -0.087 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  50 "   -0.096 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  50 "   -0.085 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  50 "   -0.074 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  TYR A  12 "    0.159 2.00e-02 2.50e+03   7.23e-02 1.57e+02
        model="  10" pdb=" CG  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 TYR A  12 "   -0.035 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 TYR A  12 "   -0.024 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 TYR A  12 "   -0.030 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="  10" pdb=" OH  TYR A  12 "    0.154 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 TYR A  12 "   -0.065 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 TYR A  12 "   -0.043 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 TYR A  12 "   -0.034 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 TYR A  12 "   -0.054 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  10" pdb=" CB  PHE A  45 "   -0.092 2.00e-02 2.50e+03   6.35e-02 1.21e+02
        model="  10" pdb=" CG  PHE A  45 "    0.015 2.00e-02 2.50e+03
        model="  10" pdb=" CD1 PHE A  45 "    0.053 2.00e-02 2.50e+03
        model="  10" pdb=" CD2 PHE A  45 "   -0.006 2.00e-02 2.50e+03
        model="  10" pdb=" CE1 PHE A  45 "   -0.029 2.00e-02 2.50e+03
        model="  10" pdb=" CE2 PHE A  45 "    0.029 2.00e-02 2.50e+03
        model="  10" pdb=" CZ  PHE A  45 "   -0.014 2.00e-02 2.50e+03
        model="  10" pdb=" HD1 PHE A  45 "    0.132 2.00e-02 2.50e+03
        model="  10" pdb=" HD2 PHE A  45 "   -0.042 2.00e-02 2.50e+03
        model="  10" pdb=" HE1 PHE A  45 "   -0.092 2.00e-02 2.50e+03
        model="  10" pdb=" HE2 PHE A  45 "    0.080 2.00e-02 2.50e+03
        model="  10" pdb=" HZ  PHE A  45 "   -0.033 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 263
        2.27 -     2.86: 5013
        2.86 -     3.44: 5432
        3.44 -     4.02: 6990
        4.02 -     4.60: 10342
  Nonbonded interactions: 28040
  Sorted by model distance:
  nonbonded model="  10" pdb="HD11 ILE A  78 "
            model="  10" pdb=" H   LYS A  85 "
     model   vdw
     1.693 2.270
  nonbonded model="  10" pdb=" HG1 THR A  83 "
            model="  10" pdb=" O   ASP A  88 "
     model   vdw
     1.793 1.850
  nonbonded model="  10" pdb=" O   GLU A  75 "
            model="  10" pdb=" HZ2 LYS A  85 "
     model   vdw
     1.796 1.850
  nonbonded model="  10" pdb=" OE2 GLU A  16 "
            model="  10" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.812 1.850
  nonbonded model="  10" pdb=" O   ILE A  30 "
            model="  10" pdb=" HG1 THR A  34 "
     model   vdw
     1.835 1.850
  ... (remaining 28035 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.043 (Z=  3.072)
  Mean delta:    0.013 (Z=  0.701)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        121.70   129.71    -8.01  1.80e+00  1.98e+01   4.5*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.30     4.30  1.00e+00  1.85e+01   4.3*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    8.012 (Z=  4.451)
  Mean delta:    1.911 (Z=  1.041)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00  -156.05   -23.95  5.00e+00  2.29e+01   4.8*sigma

  Min. delta:    0.050
  Max. delta:   87.322
  Mean delta:   19.506

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.230
  Mean delta:    0.090

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  68  TYR  CB
   A  68  TYR  CG
   A  68  TYR  CD1
   A  68  TYR  CD2
   A  68  TYR  CE1
   A  68  TYR  CE2
   A  68  TYR  CZ
   A  68  TYR  OH            0.053       0.103       56.67   5.2*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.046       0.090       42.15   4.5*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.046       0.088       42.68   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.081
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.043   2242  Z= 0.499
    Angle     :  1.759   8.012   4079  Z= 0.774
    Chirality :  0.090   0.230    176
    Planarity :  0.011   0.061    327
    Dihedral  : 15.928  87.322    769
    Min Nonbonded Distance : 1.643
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  6.57 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  8.06 %
      Allowed  :  8.87 %
      Favored  : 83.06 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.49 (0.68), residues: 137
    helix: -0.88 (0.48), residues: 82
    sheet:  None (None), residues: 0
    loop : -0.93 (0.94), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.004   HIS A 139 
   PHE   0.109   0.023   PHE A  45 
   TYR   0.131   0.025   TYR A  68 
   ARG   0.066   0.015   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.004   HIS A 139 
   PHE   0.047   0.015   PHE A  45 
   TYR   0.103   0.030   TYR A  68 
   ARG   0.011   0.003   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  93.43 %
  Rotamer outliers      =   8.06 %
  C-beta deviations     =     0
  Clashscore            =   4.51
  RMS(bonds)            =   0.0095
  RMS(angles)           =   1.76
  MolProbity score      =   2.35

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ARG   58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A LEU   93": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A ARG  129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   3"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.534, 45.038, 49.556, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.229, 61.022, 55.069, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.411, 54.866, 38.397, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.00 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.563)
  Mean delta:    0.001 (Z=  0.063)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.601 (Z=  1.392)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   84.943
  Mean delta:   23.149

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.095
  Mean delta:    0.034

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    8" pdbres="HIS A  43  conformer  : HE2, HD1 
    8" pdbres="HIS A 134  conformer  : HE2, HD1 
    8" pdbres="HIS A 135  conformer  : HE2, HD1 
    8" pdbres="HIS A 136  conformer  : HE2, HD1 
    8" pdbres="HIS A 137  conformer  : HE2, HD1 
    8" pdbres="HIS A 138  conformer  : HE2, HD1 
    8" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.046
    Angle     :  0.979   4.848   4077  Z= 0.341
    Chirality :  0.034   0.095    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.266  84.943    768
    Min Nonbonded Distance : 1.428
  
  Molprobity Statistics.
    All-atom Clashscore : 22.55
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  : 17.52 %
      Favored  : 78.83 %
    Rotamer:
      Outliers : 20.16 %
      Allowed  : 16.13 %
      Favored  : 63.71 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.40 (0.43), residues: 137
    helix: -3.71 (0.42), residues: 60
    sheet:  None (None), residues: 0
    loop : -4.96 (0.42), residues: 77
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 138 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.002   0.001   TYR A  81 
   ARG   0.001   0.000   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 138 
   PHE   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A  81 
   ARG   0.000   0.000   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 463
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   9" pdb=" N   MET A   1 "
       model="   9" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.458  0.033 2.10e-02 2.27e+03 2.45e+00
  bond model="   9" pdb=" NE  ARG A 127 "
       model="   9" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.329 -0.003 1.10e-02 8.26e+03 6.87e-02
  bond model="   9" pdb=" CZ  ARG A  21 "
       model="   9" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 4.85e-02
  bond model="   9" pdb=" CZ  ARG A 129 "
       model="   9" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.327  0.003 1.30e-02 5.92e+03 4.60e-02
  bond model="   9" pdb=" CZ  ARG A  58 "
       model="   9" pdb=" NH1 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.323  1.326 -0.003 1.40e-02 5.10e+03 4.55e-02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.90 -   106.89: 68
      106.89 -   112.89: 2717
      112.89 -   118.88: 426
      118.88 -   124.88: 824
      124.88 -   130.88: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   9" pdb=" CB  PRO A 114 "
        model="   9" pdb=" CA  PRO A 114 "
        model="   9" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.85   -4.85 3.00e+00 1.11e-01 2.61e+00
  angle model="   9" pdb=" CB  PRO A  22 "
        model="   9" pdb=" CA  PRO A  22 "
        model="   9" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.84   -4.84 3.00e+00 1.11e-01 2.61e+00
  angle model="   9" pdb=" CB  PRO A  54 "
        model="   9" pdb=" CA  PRO A  54 "
        model="   9" pdb=" HA  PRO A  54 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A 117 "
        model="   9" pdb=" CA  PRO A 117 "
        model="   9" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.81   -4.81 3.00e+00 1.11e-01 2.57e+00
  angle model="   9" pdb=" CB  PRO A   6 "
        model="   9" pdb=" CA  PRO A   6 "
        model="   9" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 878
       17.77 -    35.54: 87
       35.54 -    53.32: 44
       53.32 -    71.09: 19
       71.09 -    88.86: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   9" pdb=" CA  ASP A 103 "
           model="   9" pdb=" CB  ASP A 103 "
           model="   9" pdb=" CG  ASP A 103 "
           model="   9" pdb=" OD1 ASP A 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.93   55.93     1      2.00e+01 2.50e-03 1.06e+01
  dihedral model="   9" pdb=" CB  GLU A 133 "
           model="   9" pdb=" CG  GLU A 133 "
           model="   9" pdb=" CD  GLU A 133 "
           model="   9" pdb=" OE1 GLU A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.86  -88.86     1      3.00e+01 1.11e-03 1.05e+01
  dihedral model="   9" pdb=" CB  GLU A   8 "
           model="   9" pdb=" CG  GLU A   8 "
           model="   9" pdb=" CD  GLU A   8 "
           model="   9" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.80   85.80     1      3.00e+01 1.11e-03 9.89e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.020: 107
       0.020 -    0.039: 50
       0.039 -    0.057: 0
       0.057 -    0.076: 0
       0.076 -    0.095: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   9" pdb=" CA  ILE A  37 "
            model="   9" pdb=" N   ILE A  37 "
            model="   9" pdb=" C   ILE A  37 "
            model="   9" pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.27e-01
  chirality model="   9" pdb=" CA  ILE A   4 "
            model="   9" pdb=" N   ILE A   4 "
            model="   9" pdb=" C   ILE A   4 "
            model="   9" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.25e-01
  chirality model="   9" pdb=" CA  ILE A  38 "
            model="   9" pdb=" N   ILE A  38 "
            model="   9" pdb=" C   ILE A  38 "
            model="   9" pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.15e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  TYR A 111 "    0.000 2.00e-02 2.50e+03   1.37e-03 5.65e-02
        model="   9" pdb=" CG  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" OH  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  45 "    0.000 2.00e-02 2.50e+03   1.16e-03 4.05e-02
        model="   9" pdb=" CG  PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  45 "    0.002 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  45 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  45 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   9" pdb=" CB  PHE A  67 "    0.000 2.00e-02 2.50e+03   1.12e-03 3.74e-02
        model="   9" pdb=" CG  PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CD1 PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CD2 PHE A  67 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CE1 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" CE2 PHE A  67 "   -0.000 2.00e-02 2.50e+03
        model="   9" pdb=" CZ  PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD1 PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HD2 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HE1 PHE A  67 "   -0.003 2.00e-02 2.50e+03
        model="   9" pdb=" HE2 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   9" pdb=" HZ  PHE A  67 "    0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 247
        2.21 -     2.80: 4720
        2.80 -     3.40: 5744
        3.40 -     4.00: 7115
        4.00 -     4.60: 10818
  Nonbonded interactions: 28644
  Sorted by model distance:
  nonbonded model="   9" pdb="HD11 LEU A  93 "
            model="   9" pdb="HD13 LEU A  99 "
     model   vdw
     1.607 2.440
  nonbonded model="   9" pdb="HG12 VAL A  41 "
            model="   9" pdb="HG22 VAL A 112 "
     model   vdw
     1.632 2.440
  nonbonded model="   9" pdb="HD23 LEU A   9 "
            model="   9" pdb="HD22 LEU A  26 "
     model   vdw
     1.669 2.440
  nonbonded model="   9" pdb="HD11 ILE A   4 "
            model="   9" pdb="HG23 ILE A  30 "
     model   vdw
     1.723 2.440
  nonbonded model="   9" pdb="HD12 ILE A  37 "
            model="   9" pdb="HD23 LEU A  61 "
     model   vdw
     1.730 2.440
  ... (remaining 28639 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   3.65 %
                favored =  78.83 %
  Rotamer outliers      =  20.16 %
  C-beta deviations     =     0
  Clashscore            =  22.55
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.59

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  98  SER  CA
   A  98  SER  C           1.52     1.70    -0.17  2.10e-02  6.69e+01   8.2*sigma
   A  99  LEU  N
   A  99  LEU  CA          1.46     1.61    -0.15  1.90e-02  6.17e+01   7.9*sigma
   A  91  TYR  CA
   A  91  TYR  C           1.52     1.68    -0.15  2.10e-02  5.18e+01   7.2*sigma
   A  98  SER  C
   A  99  LEU  N           1.33     1.41    -0.08  1.40e-02  3.65e+01   6.0*sigma
   A  99  LEU  CA
   A  99  LEU  C           1.52     1.64    -0.11  2.10e-02  2.84e+01   5.3*sigma
   A  92  THR  N
   A  92  THR  CA          1.46     1.56    -0.10  1.90e-02  2.72e+01   5.2*sigma
   A  77  ILE  N
   A  77  ILE  CA          1.46     1.56    -0.10  1.90e-02  2.64e+01   5.1*sigma
   A  98  SER  N
   A  98  SER  CA          1.46     1.55    -0.09  1.90e-02  2.17e+01   4.7*sigma
   A  77  ILE  CA
   A  77  ILE  C           1.52     1.43     0.10  2.10e-02  2.15e+01   4.6*sigma
   A  91  TYR  C
   A  92  THR  N           1.33     1.39    -0.06  1.40e-02  1.89e+01   4.3*sigma
   A  76  SER  C
   A  77  ILE  N           1.33     1.39    -0.06  1.40e-02  1.66e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.172 (Z=  8.177)
  Mean delta:    0.019 (Z=  0.995)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   143.31   -21.61  1.80e+00  1.44e+02  12.0*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  C         111.00   138.58   -27.58  2.80e+00  9.70e+01   9.9*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   126.49   -16.39  1.90e+00  7.44e+01   8.6*sigma
   A  99  LEU  N
   A  99  LEU  CA
   A  99  LEU  C         111.00   134.97   -23.97  2.80e+00  7.33e+01   8.6*sigma
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        121.70   136.43   -14.73  1.80e+00  6.69e+01   8.2*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   135.64   -13.94  1.80e+00  5.99e+01   7.7*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N         116.20   131.45   -15.25  2.00e+00  5.81e+01   7.6*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   124.58   -14.48  1.90e+00  5.81e+01   7.6*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   120.74   -11.14  1.50e+00  5.51e+01   7.4*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   134.99   -13.29  1.80e+00  5.45e+01   7.4*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   134.73   -13.03  1.80e+00  5.24e+01   7.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.52   -10.62  1.50e+00  5.02e+01   7.1*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N         116.20   130.27   -14.07  2.00e+00  4.95e+01   7.0*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   121.91   -11.41  1.70e+00  4.51e+01   6.7*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50   122.63   -11.13  1.70e+00  4.29e+01   6.5*sigma
   A  89  TYR  N
   A  89  TYR  CA
   A  89  TYR  C         111.00   129.03   -18.03  2.80e+00  4.14e+01   6.4*sigma
   A  91  TYR  O
   A  91  TYR  C
   A  92  THR  N         123.00   112.93    10.07  1.60e+00  3.96e+01   6.3*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   125.22   -11.32  1.80e+00  3.95e+01   6.3*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   118.59    -5.99  1.00e+00  3.59e+01   6.0*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.56    -5.96  1.00e+00  3.55e+01   6.0*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    94.37    16.63  2.80e+00  3.53e+01   5.9*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   132.25   -10.55  1.80e+00  3.44e+01   5.9*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.22   -10.52  1.80e+00  3.42e+01   5.8*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.22   -10.52  1.80e+00  3.42e+01   5.8*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   100.82     9.68  1.70e+00  3.24e+01   5.7*sigma
   A 132  LEU  N
   A 132  LEU  CA
   A 132  LEU  CB        110.50   120.11    -9.61  1.70e+00  3.19e+01   5.7*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   119.67    -9.27  1.70e+00  2.97e+01   5.5*sigma
   A 129  ARG  C
   A 129  ARG  CA
   A 129  ARG  CB        110.10   120.43   -10.33  1.90e+00  2.96e+01   5.4*sigma
   A  98  SER  O
   A  98  SER  C
   A  99  LEU  N         123.00   114.55     8.45  1.60e+00  2.79e+01   5.3*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   130.79    -9.09  1.80e+00  2.55e+01   5.1*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   102.99     8.51  1.70e+00  2.50e+01   5.0*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   117.51    -4.91  1.00e+00  2.41e+01   4.9*sigma
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        121.70   130.40    -8.70  1.80e+00  2.34e+01   4.8*sigma
   A  99  LEU  O
   A  99  LEU  C
   A 100  GLN  N         123.00   115.36     7.64  1.60e+00  2.28e+01   4.8*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N         116.20   125.68    -9.48  2.00e+00  2.24e+01   4.7*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   130.07    -8.37  1.80e+00  2.16e+01   4.6*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   102.66     7.84  1.70e+00  2.13e+01   4.6*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   101.38     8.72  1.90e+00  2.11e+01   4.6*sigma
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        121.70   129.70    -8.00  1.80e+00  1.97e+01   4.4*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   116.16     6.84  1.60e+00  1.83e+01   4.3*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.37    -5.97  1.40e+00  1.82e+01   4.3*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30   100.79     8.51  2.00e+00  1.81e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.77e+01   4.2*sigma
   A  98  SER  CA
   A  98  SER  C
   A  98  SER  O         120.80   113.67     7.13  1.70e+00  1.76e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   116.74    -4.14  1.00e+00  1.71e+01   4.1*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   119.75    -8.15  2.00e+00  1.66e+01   4.1*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  C         111.00    99.59    11.41  2.80e+00  1.66e+01   4.1*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   108.20     8.00  2.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   27.581 (Z= 12.005)
  Mean delta:    3.082 (Z=  1.616)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   100.74    79.26  5.00e+00  2.51e+02  15.9*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -101.64   -78.36  5.00e+00  2.46e+02  15.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -102.11   -77.89  5.00e+00  2.43e+02  15.6*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   104.09    75.91  5.00e+00  2.30e+02  15.2*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   109.98    70.02  5.00e+00  1.96e+02  14.0*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   118.57    61.43  5.00e+00  1.51e+02  12.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   124.97    55.03  5.00e+00  1.21e+02  11.0*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -134.17   -45.83  5.00e+00  8.40e+01   9.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -135.51   -44.49  5.00e+00  7.92e+01   8.9*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   138.91    41.09  5.00e+00  6.75e+01   8.2*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   140.03    39.97  5.00e+00  6.39e+01   8.0*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   140.94    39.06  5.00e+00  6.10e+01   7.8*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   141.62    38.38  5.00e+00  5.89e+01   7.7*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   143.64    36.36  5.00e+00  5.29e+01   7.3*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00  -145.38   -34.62  5.00e+00  4.79e+01   6.9*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00  -145.44   -34.56  5.00e+00  4.78e+01   6.9*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   146.02    33.98  5.00e+00  4.62e+01   6.8*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   149.22    30.78  5.00e+00  3.79e+01   6.2*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00  -149.49   -30.51  5.00e+00  3.72e+01   6.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   150.82    29.18  5.00e+00  3.41e+01   5.8*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00  -151.56   -28.44  5.00e+00  3.24e+01   5.7*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   154.91    25.09  5.00e+00  2.52e+01   5.0*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   157.58    22.42  5.00e+00  2.01e+01   4.5*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   158.95    21.05  5.00e+00  1.77e+01   4.2*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   159.74    20.26  5.00e+00  1.64e+01   4.1*sigma

  Min. delta:    0.000
  Max. delta:   83.138
  Mean delta:   18.529

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.97     5.48  2.00e-01  7.50e+02  27.4*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.76     5.29  2.00e-01  6.99e+02  26.4*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.53     5.17  2.00e-01  6.69e+02  25.9*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.39     4.83  2.00e-01  5.82e+02  24.1*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -2.35     4.79  2.00e-01  5.73e+02  23.9*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -1.93     4.49  2.00e-01  5.03e+02  22.4*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.91     4.42  2.00e-01  4.89e+02  22.1*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -1.14     3.65  2.00e-01  3.33e+02  18.2*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.10     3.53  2.00e-01  3.11e+02  17.6*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     1.39     1.12  2.00e-01  3.13e+01   5.6*sigma
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51     1.65     0.86  2.00e-01  1.86e+01   4.3*sigma

  Min. delta:    0.000
  Max. delta:    5.479
  Mean delta:    1.072

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.085       0.151      142.83   7.5*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  80  GLY  O
   A  81  TYR  N             0.048       0.083       23.28   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.085
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  81  TYR  HA , Angle C-CA-HA, observed: 96.692, delta from target: 12.308
   A  51  ILE  HA , Angle CB-CA-HA, observed: 95.646, delta from target: 13.354
   A  51  ILE  HA , Angle C-CA-HA, observed: 95.316, delta from target: 13.684
   A  89  TYR  HA , Angle CB-CA-HA, observed: 122.868, delta from target: -13.868
   A  97  SER  HA , Angle CB-CA-HA, observed: 95.035, delta from target: 13.965
   A 132  LEU  HA , Angle N-CA-HA, observed: 94.947, delta from target: 15.053
   A 131  ILE  HA , Angle C-CA-HA, observed: 93.475, delta from target: 15.525
   A  91  TYR  HA , Angle N-CA-HA, observed: 127.053, delta from target: -17.053
   A  97  SER  HA , Angle C-CA-HA, observed: 90.845, delta from target: 18.155
   A  99  LEU  HA , Angle C-CA-HA, observed: 88.560, delta from target: 20.440
   A  99  LEU  HA , Angle CB-CA-HA, observed: 130.274, delta from target: -21.274
   A  98  SER  HA , Angle N-CA-HA, observed: 88.313, delta from target: 21.687
   A  92  THR  HB , Angle CA-CB-HB, observed: 86.926, delta from target: 22.074
   A  99  LEU  HA , Angle N-CA-HA, observed: 87.596, delta from target: 22.404
   A  89  TYR  HA , Angle N-CA-HA, observed: 87.252, delta from target: 22.748
   A  98  SER  HA , Angle CB-CA-HA, observed: 139.998, delta from target: -30.998
   A  98  SER  HA , Angle C-CA-HA, observed: 74.582, delta from target: 34.418

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.014   0.172   2242  Z= 0.708
    Angle     :  2.791  34.418   4079  Z= 1.205
    Chirality :  1.072   5.479    176
    Planarity :  0.012   0.085    327
    Dihedral  : 15.778  83.138    769
    Min Nonbonded Distance : 1.291
  
  Molprobity Statistics.
    All-atom Clashscore : 18.94
    Ramachandran Plot:
      Outliers :  9.49 %
      Allowed  :  8.76 %
      Favored  : 81.75 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  7.26 %
      Favored  : 85.48 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 13.74 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.55 (0.67), residues: 137
    helix: -2.21 (0.47), residues: 74
    sheet:  None (None), residues: 0
    loop : -2.46 (0.88), residues: 63
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.066   0.017   PHE A  45 
   TYR   0.199   0.022   TYR A  89 
   ARG   0.028   0.007   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A  43 
   PHE   0.046   0.018   PHE A  45 
   TYR   0.151   0.025   TYR A  89 
   ARG   0.005   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="  12" pdb=" CB  LYS A  79 "
        model="  12" pdb=" CB  LEU A  99 "
  Number of C-beta restraints generated:  260

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}
  Ramachandran outliers =   9.49 %
                favored =  81.75 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    14
  Clashscore            =  18.94
  RMS(bonds)            =   0.0136
  RMS(angles)           =   2.79
  MolProbity score      =   3.14

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.54    -0.09  1.60e-02  2.87e+01   5.4*sigma
   A  77  ILE  C
   A  78  ILE  N           1.33     1.27     0.06  1.40e-02  1.76e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.086 (Z=  5.358)
  Mean delta:    0.015 (Z=  0.791)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   139.01   -17.31  1.80e+00  9.25e+01   9.6*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    92.95    17.15  1.90e+00  8.15e+01   9.0*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   107.67    14.03  1.80e+00  6.08e+01   7.8*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   123.40   -12.90  1.70e+00  5.76e+01   7.6*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   128.69   -14.59  2.00e+00  5.32e+01   7.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.38   -10.48  1.50e+00  4.88e+01   7.0*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   123.32   -13.22  1.90e+00  4.84e+01   7.0*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   122.99     8.21  1.30e+00  3.99e+01   6.3*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60    99.36    12.24  2.00e+00  3.75e+01   6.1*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   128.03   -17.03  2.80e+00  3.70e+01   6.1*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   118.60    -6.00  1.00e+00  3.60e+01   6.0*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG1       110.40   120.60   -10.20  1.70e+00  3.60e+01   6.0*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   131.53    -9.83  1.80e+00  2.98e+01   5.5*sigma
   A  77  ILE  N
   A  77  ILE  CA
   A  77  ILE  CB        111.50   120.58    -9.08  1.70e+00  2.85e+01   5.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   130.92    -9.22  1.80e+00  2.62e+01   5.1*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.68    -5.08  1.00e+00  2.58e+01   5.1*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   130.82    -9.12  1.80e+00  2.57e+01   5.1*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.72   -10.12  2.00e+00  2.56e+01   5.1*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   113.09     8.61  1.80e+00  2.29e+01   4.8*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   130.05    -8.35  1.80e+00  2.15e+01   4.6*sigma
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        121.70   129.90    -8.20  1.80e+00  2.07e+01   4.6*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG1       110.40   118.08    -7.68  1.70e+00  2.04e+01   4.5*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   117.89    -7.39  1.70e+00  1.89e+01   4.3*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   117.83    -7.33  1.70e+00  1.86e+01   4.3*sigma
   A 116  ASP  C
   A 116  ASP  CA
   A 116  ASP  CB        110.10   118.24    -8.14  1.90e+00  1.83e+01   4.3*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   118.16    -8.06  1.90e+00  1.80e+01   4.2*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  ND1       122.70   128.96    -6.26  1.50e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.45     4.15  1.00e+00  1.72e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.52     4.08  1.00e+00  1.67e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG1       110.40   117.28    -6.88  1.70e+00  1.64e+01   4.0*sigma
   A  77  ILE  O
   A  77  ILE  C
   A  78  ILE  N         123.00   116.56     6.44  1.60e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:   17.309 (Z=  9.616)
  Mean delta:    2.642 (Z=  1.442)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   -94.30   -85.70  5.00e+00  2.94e+02  17.1*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -95.83   -84.17  5.00e+00  2.83e+02  16.8*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -96.98   -83.02  5.00e+00  2.76e+02  16.6*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -116.69   -63.31  5.00e+00  1.60e+02  12.7*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   116.70    63.30  5.00e+00  1.60e+02  12.7*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   129.17    50.83  5.00e+00  1.03e+02  10.2*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   140.94    39.06  5.00e+00  6.10e+01   7.8*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   143.64    36.36  5.00e+00  5.29e+01   7.3*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   145.76    34.24  5.00e+00  4.69e+01   6.8*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00   149.63    30.37  5.00e+00  3.69e+01   6.1*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -149.66   -30.34  5.00e+00  3.68e+01   6.1*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   151.65    28.35  5.00e+00  3.22e+01   5.7*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   156.47    23.53  5.00e+00  2.21e+01   4.7*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -156.96   -23.04  5.00e+00  2.12e+01   4.6*sigma
   A  50  TYR  CA
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        180.00   157.43    22.57  5.00e+00  2.04e+01   4.5*sigma

  Min. delta:    0.056
  Max. delta:   85.703
  Mean delta:   17.021

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.13     5.65  2.00e-01  7.97e+02  28.2*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.71     5.35  2.00e-01  7.16e+02  26.8*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.49     5.13  2.00e-01  6.58e+02  25.7*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.08     4.59  2.00e-01  5.27e+02  23.0*sigma
   A 116  ASP  CA
   A 116  ASP  N
   A 116  ASP  C
   A 116  ASP  CB          2.51    -2.00     4.51  2.00e-01  5.08e+02  22.5*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.14     3.57  2.00e-01  3.19e+02  17.9*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -0.66     3.10  2.00e-01  2.40e+02  15.5*sigma
   A  82  THR  CA
   A  82  THR  N
   A  82  THR  C
   A  82  THR  CB          2.53     1.65     0.87  2.00e-01  1.91e+01   4.4*sigma

  Min. delta:    0.000
  Max. delta:    5.645
  Mean delta:    0.939

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.308       0.611     1901.03  30.5*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  ND1
   A  43  HIS  CD2
   A  43  HIS  CE1
   A  43  HIS  NE2           0.068       0.092       69.94   4.6*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.048       0.084       45.47   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.308
  Mean delta:    0.027

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  71  ILE  HB , Angle CA-CB-HB, observed: 96.580, delta from target: 12.420
   A  74  ASP  HA , Angle CB-CA-HA, observed: 95.165, delta from target: 13.835
   A  77  ILE  HA , Angle C-CA-HA, observed: 122.943, delta from target: -13.943
   A  51  ILE  HA , Angle C-CA-HA, observed: 94.866, delta from target: 14.134
   A  82  THR  HA , Angle N-CA-HA, observed: 95.527, delta from target: 14.473
   A  78  ILE  HA , Angle CB-CA-HA, observed: 124.228, delta from target: -15.228
   A  79  LYS  HA , Angle CB-CA-HA, observed: 125.692, delta from target: -16.692
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.006, delta from target: 16.994
   A  78  ILE  HA , Angle N-CA-HA, observed: 84.404, delta from target: 25.596
   A  78  ILE  HA , Angle C-CA-HA, observed: 78.901, delta from target: 30.099

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.086   2242  Z= 0.563
    Angle     :  2.407  30.099   4079  Z= 1.066
    Chirality :  0.939   5.645    176
    Planarity :  0.020   0.306    327
    Dihedral  : 13.947  85.703    769
    Min Nonbonded Distance : 1.505
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  5.11 %
      Allowed  :  5.84 %
      Favored  : 89.05 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  5.65 %
      Favored  : 89.52 %
    Cbeta Deviations :  7.58 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 7.63 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.49 (0.62), residues: 137
    helix: -2.36 (0.49), residues: 75
    sheet:  None (None), residues: 0
    loop : -2.13 (0.75), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A  43 
   PHE   0.034   0.009   PHE A  67 
   TYR   0.806   0.043   TYR A  91 
   ARG   0.037   0.006   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A  43 
   PHE   0.020   0.007   PHE A  67 
   TYR   0.611   0.051   TYR A  91 
   ARG   0.004   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A LEU    9": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A VAL   14": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ARG   21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   36": "OD1" <-> "OD2"
    Residue "A VAL   41": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A LEU   53": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   59": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A LEU   64": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   74": "OD1" <-> "OD2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    Residue "A LEU   99": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A VAL  104": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A ARG  127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   1"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 71
        1.23 -     1.42: 401
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="  12" pdb=" CD2 HIS A 135 "
       model="  12" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.406 -0.032 1.10e-02 8.26e+03 8.26e+00
  bond model="  12" pdb=" CD2 HIS A 136 "
       model="  12" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 8.09e+00
  bond model="  12" pdb=" CD2 HIS A 139 "
       model="  12" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.33e+00
  bond model="  12" pdb=" CD2 HIS A 137 "
       model="  12" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.13e+00
  bond model="  12" pdb=" CZ  ARG A  21 "
       model="  12" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.79e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       90.97 -    99.28: 5
       99.28 -   107.60: 489
      107.60 -   115.92: 2508
      115.92 -   124.24: 959
      124.24 -   132.56: 118
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="  12" pdb=" N   LYS A  79 "
        model="  12" pdb=" CA  LYS A  79 "
        model="  12" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.50  120.85  -10.35 1.70e+00 3.46e-01 3.71e+01
  angle model="  12" pdb=" C   ILE A  78 "
        model="  12" pdb=" N   LYS A  79 "
        model="  12" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  132.56  -10.86 1.80e+00 3.09e-01 3.64e+01
  angle model="  12" pdb=" C   LEU A  99 "
        model="  12" pdb=" CA  LEU A  99 "
        model="  12" pdb=" HA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     109.00   90.97   18.03 3.00e+00 1.11e-01 3.61e+01
  angle model="  12" pdb=" CA  ASP A 103 "
        model="  12" pdb=" CB  ASP A 103 "
        model="  12" pdb=" CG  ASP A 103 "
      ideal   model   delta    sigma   weight residual
     112.60  106.63    5.97 1.00e+00 1.00e+00 3.56e+01
  angle model="  12" pdb=" C   SER A  98 "
        model="  12" pdb=" N   LEU A  99 "
        model="  12" pdb=" CA  LEU A  99 "
      ideal   model   delta    sigma   weight residual
     121.70  132.21  -10.51 1.80e+00 3.09e-01 3.41e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.12: 947
       18.12 -    36.24: 47
       36.24 -    54.35: 23
       54.35 -    72.47: 4
       72.47 -    90.59: 8
  Dihedral angle restraints: 1029
    sinusoidal: 562
      harmonic: 467
  Sorted by residual:
  dihedral model="  12" pdb=" CA  LEU A  93 "
           model="  12" pdb=" C   LEU A  93 "
           model="  12" pdb=" N   GLY A  94 "
           model="  12" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   89.41   90.59     0      5.00e+00 4.00e-02 3.28e+02
  dihedral model="  12" pdb=" CA  ILE A  78 "
           model="  12" pdb=" C   ILE A  78 "
           model="  12" pdb=" N   LYS A  79 "
           model="  12" pdb=" CA  LYS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -138.06  -41.94     0      5.00e+00 4.00e-02 7.04e+01
  dihedral model="  12" pdb=" CA  GLY A  96 "
           model="  12" pdb=" C   GLY A  96 "
           model="  12" pdb=" N   SER A  97 "
           model="  12" pdb=" CA  SER A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -139.97  -40.03     0      5.00e+00 4.00e-02 6.41e+01
  ... (remaining 1026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.746: 174
       0.746 -    1.491: 0
       1.491 -    2.237: 0
       2.237 -    2.982: 0
       2.982 -    3.728: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="  12" pdb=" CA  LEU A  99 "
            model="  12" pdb=" N   LEU A  99 "
            model="  12" pdb=" C   LEU A  99 "
            model="  12" pdb=" CB  LEU A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.22    3.73 2.00e-01 2.50e+01 3.47e+02
  chirality model="  12" pdb=" CA  LYS A  79 "
            model="  12" pdb=" N   LYS A  79 "
            model="  12" pdb=" C   LYS A  79 "
            model="  12" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -1.14    3.65 2.00e-01 2.50e+01 3.33e+02
  chirality model="  12" pdb=" CA  THR A  82 "
            model="  12" pdb=" N   THR A  82 "
            model="  12" pdb=" C   THR A  82 "
            model="  12" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.02    0.50 2.00e-01 2.50e+01 6.30e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A  50 "    0.121 2.00e-02 2.50e+03   6.33e-02 1.20e+02
        model="  12" pdb=" CG  TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A  50 "   -0.034 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A  50 "   -0.039 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A  50 "    0.143 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A  50 "   -0.058 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A  50 "   -0.079 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  TYR A 111 "    0.116 2.00e-02 2.50e+03   4.60e-02 6.34e+01
        model="  12" pdb=" CG  TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="  12" pdb=" CD1 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 TYR A 111 "   -0.030 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="  12" pdb=" CE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="  12" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="  12" pdb=" OH  TYR A 111 "    0.076 2.00e-02 2.50e+03
        model="  12" pdb=" HD1 TYR A 111 "   -0.031 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 TYR A 111 "   -0.052 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="  12" pdb=" HE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="  12" pdb=" CB  HIS A 136 "    0.058 2.00e-02 2.50e+03   4.54e-02 4.12e+01
        model="  12" pdb=" CG  HIS A 136 "   -0.058 2.00e-02 2.50e+03
        model="  12" pdb=" ND1 HIS A 136 "   -0.057 2.00e-02 2.50e+03
        model="  12" pdb=" CD2 HIS A 136 "   -0.010 2.00e-02 2.50e+03
        model="  12" pdb=" CE1 HIS A 136 "    0.005 2.00e-02 2.50e+03
        model="  12" pdb=" NE2 HIS A 136 "   -0.034 2.00e-02 2.50e+03
        model="  12" pdb=" HD2 HIS A 136 "    0.030 2.00e-02 2.50e+03
        model="  12" pdb=" HE1 HIS A 136 "    0.066 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.35: 564
        2.35 -     2.91: 5128
        2.91 -     3.47: 5402
        3.47 -     4.04: 7258
        4.04 -     4.60: 10552
  Nonbonded interactions: 28904
  Sorted by model distance:
  nonbonded model="  12" pdb=" HB3 ALA A 115 "
            model="  12" pdb=" H   HIS A 138 "
     model   vdw
     1.784 2.270
  nonbonded model="  12" pdb=" HZ3 LYS A  10 "
            model="  12" pdb=" OD1 ASP A  23 "
     model   vdw
     1.816 1.850
  nonbonded model="  12" pdb=" OE2 GLU A  16 "
            model="  12" pdb=" HZ2 LYS A  19 "
     model   vdw
     1.835 1.850
  nonbonded model="  12" pdb=" O   LEU A  61 "
            model="  12" pdb=" HG  SER A  65 "
     model   vdw
     1.836 1.850
  nonbonded model="  12" pdb=" HZ1 LYS A  40 "
            model="  12" pdb=" O   GLU A  84 "
     model   vdw
     1.863 1.850
  ... (remaining 28899 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   5.11 %
                favored =  89.05 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =    10
  Clashscore            =   8.12
  RMS(bonds)            =   0.0108
  RMS(angles)           =   2.41
  MolProbity score      =   2.54

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ILE A  77 "
        model="   2" pdb=" CB  ILE A  78 "
        model="   2" pdb=" CB  ILE A 122 "
        model="   2" pdb=" CB  VAL A 126 "
        model="   2" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.45, 44.288, 58.506, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 41
        1.23 -     1.42: 434
        1.42 -     1.62: 657
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" N   ARG A 127 "
       model="   2" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.340  0.118 1.90e-02 2.77e+03 3.86e+01
  bond model="   2" pdb=" CA  VAL A 126 "
       model="   2" pdb=" C   VAL A 126 "
    ideal  model  delta    sigma   weight residual
    1.525  1.441  0.084 2.10e-02 2.27e+03 1.61e+01
  bond model="   2" pdb=" N   LYS A 125 "
       model="   2" pdb=" CA  LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.526 -0.068 1.90e-02 2.77e+03 1.27e+01
  bond model="   2" pdb=" C   VAL A 126 "
       model="   2" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.286  0.043 1.40e-02 5.10e+03 9.43e+00
  bond model="   2" pdb=" CA  THR A  92 "
       model="   2" pdb=" C   THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.525  1.463  0.062 2.10e-02 2.27e+03 8.76e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       81.22 -    92.03: 2
       92.03 -   102.84: 37
      102.84 -   113.65: 2763
      113.65 -   124.46: 1155
      124.46 -   135.27: 122
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" CA  VAL A 126 "
        model="   2" pdb=" C   VAL A 126 "
        model="   2" pdb=" N   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     116.20   96.03   20.17 2.00e+00 2.50e-01 1.02e+02
  angle model="   2" pdb=" C   ILE A 122 "
        model="   2" pdb=" CA  ILE A 122 "
        model="   2" pdb=" HA  ILE A 122 "
      ideal   model   delta    sigma   weight residual
     109.00   81.22   27.78 3.00e+00 1.11e-01 8.58e+01
  angle model="   2" pdb=" CA  ILE A  51 "
        model="   2" pdb=" C   ILE A  51 "
        model="   2" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  128.34  -11.44 1.50e+00 4.44e-01 5.81e+01
  angle model="   2" pdb=" C   ARG A 127 "
        model="   2" pdb=" CA  ARG A 127 "
        model="   2" pdb=" CB  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     110.10  124.57  -14.47 1.90e+00 2.77e-01 5.80e+01
  angle model="   2" pdb=" C   ILE A  78 "
        model="   2" pdb=" N   LYS A  79 "
        model="   2" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  135.27  -13.57 1.80e+00 3.09e-01 5.69e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.65: 947
       19.65 -    39.29: 47
       39.29 -    58.94: 21
       58.94 -    78.59: 3
       78.59 -    98.23: 3
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   2" pdb=" CA  ILE A 122 "
           model="   2" pdb=" C   ILE A 122 "
           model="   2" pdb=" N   GLU A 123 "
           model="   2" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   81.77   98.23     0      5.00e+00 4.00e-02 3.86e+02
  dihedral model="   2" pdb=" CA  GLU A 123 "
           model="   2" pdb=" C   GLU A 123 "
           model="   2" pdb=" N   ALA A 124 "
           model="   2" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   96.90   83.10     0      5.00e+00 4.00e-02 2.76e+02
  dihedral model="   2" pdb=" CA  LYS A 125 "
           model="   2" pdb=" C   LYS A 125 "
           model="   2" pdb=" N   VAL A 126 "
           model="   2" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  101.98   78.02     0      5.00e+00 4.00e-02 2.43e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.058: 169
       1.058 -    2.116: 0
       2.116 -    3.173: 0
       3.173 -    4.231: 2
       4.231 -    5.289: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CB  ILE A  78 "
            model="   2" pdb=" CA  ILE A  78 "
            model="   2" pdb=" CG1 ILE A  78 "
            model="   2" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.64    5.29 2.00e-01 2.50e+01 6.99e+02
  chirality model="   2" pdb=" CA  HIS A 139 "
            model="   2" pdb=" N   HIS A 139 "
            model="   2" pdb=" C   HIS A 139 "
            model="   2" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.38    4.89 2.00e-01 2.50e+01 5.98e+02
  chirality model="   2" pdb=" CA  VAL A 126 "
            model="   2" pdb=" N   VAL A 126 "
            model="   2" pdb=" C   VAL A 126 "
            model="   2" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44   -2.31    4.75 2.00e-01 2.50e+01 5.65e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  89 "   -0.089 2.00e-02 2.50e+03   3.52e-02 3.72e+01
        model="   2" pdb=" CG  TYR A  89 "    0.019 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  89 "    0.022 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  89 "    0.019 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  89 "    0.007 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  89 "    0.011 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  89 "   -0.060 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  89 "    0.034 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  89 "    0.024 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  89 "    0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  12 "    0.063 2.00e-02 2.50e+03   3.41e-02 3.49e+01
        model="   2" pdb=" CG  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  12 "    0.070 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  12 "   -0.040 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  12 "   -0.049 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  PHE A  15 "   -0.078 2.00e-02 2.50e+03   3.39e-02 3.44e+01
        model="   2" pdb=" CG  PHE A  15 "    0.028 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 PHE A  15 "    0.019 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 PHE A  15 "    0.026 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 PHE A  15 "   -0.004 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 PHE A  15 "   -0.011 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 PHE A  15 "    0.028 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 PHE A  15 "    0.049 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 PHE A  15 "   -0.022 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 PHE A  15 "   -0.043 2.00e-02 2.50e+03
        model="   2" pdb=" HZ  PHE A  15 "    0.009 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 415
        2.31 -     2.88: 5170
        2.88 -     3.45: 5715
        3.45 -     4.03: 7517
        4.03 -     4.60: 10995
  Nonbonded interactions: 29812
  Sorted by model distance:
  nonbonded model="   2" pdb=" OD1 ASP A  95 "
            model="   2" pdb=" HG  SER A  97 "
     model   vdw
     1.735 1.850
  nonbonded model="   2" pdb=" HA  VAL A 126 "
            model="   2" pdb=" H   ARG A 127 "
     model   vdw
     1.748 2.270
  nonbonded model="   2" pdb=" HA  ALA A 124 "
            model="   2" pdb=" HA  VAL A 126 "
     model   vdw
     1.758 2.440
  nonbonded model="   2" pdb="HG22 ILE A  77 "
            model="   2" pdb=" H   ILE A  78 "
     model   vdw
     1.769 2.270
  nonbonded model="   2" pdb=" OD1 ASP A  44 "
            model="   2" pdb=" HG  SER A  46 "
     model   vdw
     1.778 1.850
  ... (remaining 29807 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.59    -0.14  1.60e-02  7.18e+01   8.5*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.61    -0.09  2.10e-02  1.76e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.136 (Z=  8.473)
  Mean delta:    0.017 (Z=  0.886)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  C
   A 125  LYS  CA
   A 125  LYS  CB        110.10   129.17   -19.07  1.90e+00  1.01e+02  10.0*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   137.55   -15.85  1.80e+00  7.75e+01   8.8*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   137.40   -15.70  1.80e+00  7.61e+01   8.7*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   124.86   -14.36  1.70e+00  7.14e+01   8.4*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   129.69   -15.59  2.00e+00  6.07e+01   7.8*sigma
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        121.70   135.65   -13.95  1.80e+00  6.01e+01   7.8*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   124.45   -14.35  1.90e+00  5.70e+01   7.6*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   124.30   -12.80  1.70e+00  5.67e+01   7.5*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   108.18    13.52  1.80e+00  5.64e+01   7.5*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   126.37   -12.47  1.80e+00  4.80e+01   6.9*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10   122.85   -12.75  1.90e+00  4.50e+01   6.7*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   133.74   -12.04  1.80e+00  4.48e+01   6.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   133.48   -11.78  1.80e+00  4.29e+01   6.5*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   132.71   -11.01  1.80e+00  3.74e+01   6.1*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    94.49    16.51  2.80e+00  3.48e+01   5.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.43    -5.83  1.00e+00  3.39e+01   5.8*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   125.54    -8.64  1.50e+00  3.32e+01   5.8*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   132.00   -10.30  1.80e+00  3.28e+01   5.7*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   126.87   -15.87  2.80e+00  3.21e+01   5.7*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   120.30   -10.20  1.90e+00  2.88e+01   5.4*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   130.88    -9.18  1.80e+00  2.60e+01   5.1*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   112.80     8.90  1.80e+00  2.44e+01   4.9*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   130.48    -8.78  1.80e+00  2.38e+01   4.9*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   106.45     9.75  2.00e+00  2.38e+01   4.9*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG1       110.40   118.68    -8.28  1.70e+00  2.37e+01   4.9*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00    97.38    13.62  2.80e+00  2.37e+01   4.9*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   117.45    -4.85  1.00e+00  2.35e+01   4.8*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG1       110.40   118.51    -8.11  1.70e+00  2.28e+01   4.8*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   130.11    -8.41  1.80e+00  2.19e+01   4.7*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   112.87     7.93  1.70e+00  2.17e+01   4.7*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   118.42    -7.92  1.70e+00  2.17e+01   4.7*sigma
   A  78  ILE  CB
   A  78  ILE  CG1
   A  78  ILE  CD1       113.80   123.56    -9.76  2.10e+00  2.16e+01   4.6*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   130.06    -8.36  1.80e+00  2.16e+01   4.6*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   129.97    -8.27  1.80e+00  2.11e+01   4.6*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   129.82    -8.12  1.80e+00  2.03e+01   4.5*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   118.14    -7.64  1.70e+00  2.02e+01   4.5*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 122  ILE  O         120.80   128.35    -7.55  1.70e+00  1.97e+01   4.4*sigma
   A  93  LEU  CA
   A  93  LEU  CB
   A  93  LEU  CG        116.30   131.22   -14.92  3.50e+00  1.82e+01   4.3*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.81     5.39  1.30e+00  1.72e+01   4.1*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   103.32     8.28  2.00e+00  1.71e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.71e+01   4.1*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   129.09    -7.39  1.80e+00  1.68e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N         116.20   108.01     8.19  2.00e+00  1.68e+01   4.1*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   117.87    -7.77  1.90e+00  1.67e+01   4.1*sigma
   A 117  PRO  N
   A 117  PRO  CA
   A 117  PRO  C         112.10   122.28   -10.18  2.50e+00  1.66e+01   4.1*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD2       110.70   122.79   -12.09  3.00e+00  1.62e+01   4.0*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.04    -5.64  1.40e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   19.065 (Z= 10.034)
  Mean delta:    2.899 (Z=  1.550)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    49.83   130.17  5.00e+00  6.78e+02  26.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00    76.84   103.16  5.00e+00  4.26e+02  20.6*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -91.90   -88.10  5.00e+00  3.10e+02  17.6*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    93.82    86.18  5.00e+00  2.97e+02  17.2*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -124.68   -55.32  5.00e+00  1.22e+02  11.1*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   130.43    49.57  5.00e+00  9.83e+01   9.9*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   130.44    49.56  5.00e+00  9.82e+01   9.9*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   138.18    41.82  5.00e+00  6.99e+01   8.4*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   139.56    40.44  5.00e+00  6.54e+01   8.1*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   141.85    38.15  5.00e+00  5.82e+01   7.6*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   144.34    35.66  5.00e+00  5.09e+01   7.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA          0.00   -35.11    35.11  5.00e+00  4.93e+01   7.0*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   147.52    32.48  5.00e+00  4.22e+01   6.5*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   148.82    31.18  5.00e+00  3.89e+01   6.2*sigma
   A  50  TYR  CA
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        180.00  -150.05   -29.95  5.00e+00  3.59e+01   6.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00  -153.10   -26.90  5.00e+00  2.90e+01   5.4*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   153.35    26.65  5.00e+00  2.84e+01   5.3*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00  -154.25   -25.75  5.00e+00  2.65e+01   5.1*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   154.36    25.64  5.00e+00  2.63e+01   5.1*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   155.24    24.76  5.00e+00  2.45e+01   5.0*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -156.91   -23.09  5.00e+00  2.13e+01   4.6*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -158.47   -21.53  5.00e+00  1.85e+01   4.3*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00  -158.74   -21.26  5.00e+00  1.81e+01   4.3*sigma
   A  38  ILE  CA
   A  38  ILE  C
   A  39  LEU  N
   A  39  LEU  CA        180.00   159.16    20.84  5.00e+00  1.74e+01   4.2*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -159.58   -20.42  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.030
  Max. delta:  130.173
  Mean delta:   19.857

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -2.97     5.40  2.00e-01  7.29e+02  27.0*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  C
   A  52  PRO  CB          2.72    -2.39     5.11  2.00e-01  6.53e+02  25.5*sigma
   A 128  MET  CA
   A 128  MET  N
   A 128  MET  C
   A 128  MET  CB          2.51    -2.54     5.05  2.00e-01  6.38e+02  25.2*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.51     5.02  2.00e-01  6.30e+02  25.1*sigma
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.20     4.84  2.00e-01  5.86e+02  24.2*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -2.27     4.78  2.00e-01  5.72e+02  23.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -2.21     4.64  2.00e-01  5.39e+02  23.2*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     0.59     1.92  2.00e-01  9.25e+01   9.6*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51     1.24     1.27  2.00e-01  4.06e+01   6.4*sigma

  Min. delta:    0.001
  Max. delta:    5.400
  Mean delta:    1.020

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  79  LYS  O
   A  80  GLY  N             0.058       0.100       33.44   5.0*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.076       0.080      116.98   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.086
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    7" pdbres="HIS A  43  conformer  : HE2, HD1 
    7" pdbres="HIS A 134  conformer  : HE2, HD1 
    7" pdbres="HIS A 135  conformer  : HE2, HD1 
    7" pdbres="HIS A 136  conformer  : HE2, HD1 
    7" pdbres="HIS A 137  conformer  : HE2, HD1 
    7" pdbres="HIS A 138  conformer  : HE2, HD1 
    7" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  93  LEU  HG , Angle CB-CG-HG, observed: 96.866, delta from target: 12.134
   A  77  ILE  HB , Angle CA-CB-HB, observed: 96.803, delta from target: 12.197
   A  91  TYR  HA , Angle CB-CA-HA, observed: 96.667, delta from target: 12.333
   A 127  ARG  HA , Angle C-CA-HA, observed: 95.932, delta from target: 13.068
   A  90  SER  HA , Angle N-CA-HA, observed: 96.788, delta from target: 13.212
   A 126  VAL  HA , Angle CB-CA-HA, observed: 95.725, delta from target: 13.275
   A 127  ARG  HA , Angle N-CA-HA, observed: 96.133, delta from target: 13.867
   A  81  TYR  HA , Angle CB-CA-HA, observed: 93.439, delta from target: 15.561
   A 125  LYS  HA , Angle CB-CA-HA, observed: 92.909, delta from target: 16.091
   A 125  LYS  HA , Angle N-CA-HA, observed: 126.928, delta from target: -16.928
   A  79  LYS  HA , Angle N-CA-HA, observed: 126.977, delta from target: -16.977
   A  91  TYR  HA , Angle N-CA-HA, observed: 86.849, delta from target: 23.151
   A  81  TYR  HA , Angle C-CA-HA, observed: 80.259, delta from target: 28.741

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.136   2242  Z= 0.631
    Angle     :  2.550  28.741   4079  Z= 1.130
    Chirality :  1.020   5.400    176
    Planarity :  0.014   0.086    327
    Dihedral  : 16.058 130.173    769
    Min Nonbonded Distance : 1.582
  
  Molprobity Statistics.
    All-atom Clashscore : 19.39
    Ramachandran Plot:
      Outliers : 10.95 %
      Allowed  :  8.03 %
      Favored  : 81.02 %
    Rotamer:
      Outliers : 14.52 %
      Allowed  :  2.42 %
      Favored  : 83.06 %
    Cbeta Deviations :  9.85 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 2.29 %
      Twisted Proline : 14.29 %
      Twisted General : 9.92 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.42 (0.61), residues: 137
    helix: -1.16 (0.53), residues: 64
    sheet:  None (None), residues: 0
    loop : -3.47 (0.65), residues: 73
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.003   HIS A  43 
   PHE   0.074   0.013   PHE A  67 
   TYR   0.169   0.022   TYR A  91 
   ARG   0.039   0.007   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.003   HIS A  43 
   PHE   0.052   0.013   PHE A  67 
   TYR   0.134   0.025   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =  10.95 %
                favored =  81.02 %
  Rotamer outliers      =  14.52 %
  C-beta deviations     =    13
  Clashscore            =  19.39
  RMS(bonds)            =   0.0121
  RMS(angles)           =   2.55
  MolProbity score      =   3.39

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   2" pdb=" CB  ILE A  51 "
        model="   2" pdb=" CB  ASP A  74 "
        model="   2" pdb=" CB  LYS A  79 "
        model="   2" pdb=" CB  TYR A  89 "
        model="   2" pdb=" CB  SER A  90 "
        model="   2" pdb=" CB  THR A  92 "
        model="   2" pdb=" CB  LEU A  93 "
        model="   2" pdb=" CB  SER A  98 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 56
        1.23 -     1.43: 418
        1.43 -     1.62: 658
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   2" pdb=" N   THR A  92 "
       model="   2" pdb=" CA  THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.458  1.553 -0.095 1.90e-02 2.77e+03 2.52e+01
  bond model="   2" pdb=" N   LYS A  79 "
       model="   2" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.552 -0.094 1.90e-02 2.77e+03 2.43e+01
  bond model="   2" pdb=" CB  THR A  92 "
       model="   2" pdb=" OG1 THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.433  1.356  0.077 1.60e-02 3.91e+03 2.29e+01
  bond model="   2" pdb=" C   ILE A  78 "
       model="   2" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.394 -0.065 1.40e-02 5.10e+03 2.16e+01
  bond model="   2" pdb=" CA  ILE A  78 "
       model="   2" pdb=" C   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.525  1.610 -0.085 2.10e-02 2.27e+03 1.64e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       93.23 -   101.90: 31
      101.90 -   110.56: 2225
      110.56 -   119.23: 934
      119.23 -   127.89: 875
      127.89 -   136.56: 14
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   2" pdb=" C   TYR A  91 "
        model="   2" pdb=" N   THR A  92 "
        model="   2" pdb=" CA  THR A  92 "
      ideal   model   delta    sigma   weight residual
     121.70  136.56  -14.86 1.80e+00 3.09e-01 6.81e+01
  angle model="   2" pdb=" CA  ILE A  51 "
        model="   2" pdb=" C   ILE A  51 "
        model="   2" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  128.18  -11.28 1.50e+00 4.44e-01 5.65e+01
  angle model="   2" pdb=" C   ASP A  88 "
        model="   2" pdb=" N   TYR A  89 "
        model="   2" pdb=" CA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     121.70  134.14  -12.44 1.80e+00 3.09e-01 4.77e+01
  angle model="   2" pdb=" CA  THR A  82 "
        model="   2" pdb=" CB  THR A  82 "
        model="   2" pdb=" OG1 THR A  82 "
      ideal   model   delta    sigma   weight residual
     109.60  119.95  -10.35 1.50e+00 4.44e-01 4.76e+01
  angle model="   2" pdb=" C   TYR A  50 "
        model="   2" pdb=" N   ILE A  51 "
        model="   2" pdb=" CA  ILE A  51 "
      ideal   model   delta    sigma   weight residual
     121.70  132.53  -10.83 1.80e+00 3.09e-01 3.62e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.48: 932
       18.48 -    36.96: 54
       36.96 -    55.44: 21
       55.44 -    73.92: 8
       73.92 -    92.39: 2
  Dihedral angle restraints: 1017
    sinusoidal: 562
      harmonic: 455
  Sorted by residual:
  dihedral model="   2" pdb=" CA  LEU A  93 "
           model="   2" pdb=" C   LEU A  93 "
           model="   2" pdb=" N   GLY A  94 "
           model="   2" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -87.61  -92.39     0      5.00e+00 4.00e-02 3.41e+02
  dihedral model="   2" pdb=" CA  TYR A  89 "
           model="   2" pdb=" C   TYR A  89 "
           model="   2" pdb=" N   SER A  90 "
           model="   2" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -99.28  -80.72     0      5.00e+00 4.00e-02 2.61e+02
  dihedral model="   2" pdb=" CA  ILE A  78 "
           model="   2" pdb=" C   ILE A  78 "
           model="   2" pdb=" N   LYS A  79 "
           model="   2" pdb=" CA  LYS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  106.24   73.76     0      5.00e+00 4.00e-02 2.18e+02
  ... (remaining 1014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.172: 168
       1.172 -    2.345: 0
       2.345 -    3.517: 0
       3.517 -    4.689: 3
       4.689 -    5.862: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   2" pdb=" CA  LYS A  79 "
            model="   2" pdb=" N   LYS A  79 "
            model="   2" pdb=" C   LYS A  79 "
            model="   2" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.35    5.86 2.00e-01 2.50e+01 8.59e+02
  chirality model="   2" pdb=" CA  THR A  92 "
            model="   2" pdb=" N   THR A  92 "
            model="   2" pdb=" C   THR A  92 "
            model="   2" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53   -3.21    5.73 2.00e-01 2.50e+01 8.22e+02
  chirality model="   2" pdb=" CA  LEU A  93 "
            model="   2" pdb=" N   LEU A  93 "
            model="   2" pdb=" C   LEU A  93 "
            model="   2" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.73    5.24 2.00e-01 2.50e+01 6.86e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  89 "    0.133 2.00e-02 2.50e+03   5.73e-02 9.84e+01
        model="   2" pdb=" CG  TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  89 "   -0.028 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  89 "   -0.028 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  89 "   -0.012 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  89 "   -0.012 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  89 "    0.027 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  89 "    0.094 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  89 "   -0.066 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  89 "   -0.065 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  89 "   -0.027 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  89 "   -0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A 111 "    0.131 2.00e-02 2.50e+03   5.09e-02 7.77e+01
        model="   2" pdb=" CG  TYR A 111 "   -0.028 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A 111 "   -0.029 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A 111 "   -0.031 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A 111 "    0.080 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A 111 "   -0.043 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A 111 "   -0.048 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A 111 "   -0.010 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   2" pdb=" CB  TYR A  81 "    0.121 2.00e-02 2.50e+03   4.93e-02 7.29e+01
        model="   2" pdb=" CG  TYR A  81 "   -0.068 2.00e-02 2.50e+03
        model="   2" pdb=" CD1 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   2" pdb=" CD2 TYR A  81 "   -0.043 2.00e-02 2.50e+03
        model="   2" pdb=" CE1 TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   2" pdb=" CE2 TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="   2" pdb=" CZ  TYR A  81 "    0.011 2.00e-02 2.50e+03
        model="   2" pdb=" OH  TYR A  81 "    0.040 2.00e-02 2.50e+03
        model="   2" pdb=" HD1 TYR A  81 "    0.004 2.00e-02 2.50e+03
        model="   2" pdb=" HD2 TYR A  81 "   -0.060 2.00e-02 2.50e+03
        model="   2" pdb=" HE1 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   2" pdb=" HE2 TYR A  81 "    0.041 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 393
        2.30 -     2.88: 5186
        2.88 -     3.45: 5902
        3.45 -     4.03: 7678
        4.03 -     4.60: 11427
  Nonbonded interactions: 30586
  Sorted by model distance:
  nonbonded model="   2" pdb=" HB3 LYS A  79 "
            model="   2" pdb=" HA  THR A  82 "
     model   vdw
     1.726 2.440
  nonbonded model="   2" pdb=" H   LYS A  79 "
            model="   2" pdb="HG21 THR A  92 "
     model   vdw
     1.729 2.270
  nonbonded model="   2" pdb=" O   LEU A  61 "
            model="   2" pdb=" HG  SER A  65 "
     model   vdw
     1.795 1.850
  nonbonded model="   2" pdb="HG23 VAL A  41 "
            model="   2" pdb=" H   HIS A  43 "
     model   vdw
     1.838 2.270
  nonbonded model="   2" pdb=" OD2 ASP A  95 "
            model="   2" pdb=" HG  SER A  97 "
     model   vdw
     1.843 1.850
  ... (remaining 30581 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (58.693, 47.251, 47.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  ASP A  74 "
        model="   1" pdb=" CB  ILE A  78 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CB  TYR A  89 "
        model="   1" pdb=" CB  THR A  92 "
  Number of C-beta restraints generated:  252

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 75
        1.23 -     1.43: 397
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   1" pdb=" CB  THR A  82 "
       model="   1" pdb=" OG1 THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.433  1.371  0.062 1.60e-02 3.91e+03 1.52e+01
  bond model="   1" pdb=" N   GLY A  80 "
       model="   1" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.511 -0.060 1.60e-02 3.91e+03 1.41e+01
  bond model="   1" pdb=" CA  ASP A  88 "
       model="   1" pdb=" C   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.597 -0.072 2.10e-02 2.27e+03 1.17e+01
  bond model="   1" pdb=" CB  LYS A  79 "
       model="   1" pdb=" CG  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.520  1.613 -0.093 3.00e-02 1.11e+03 9.65e+00
  bond model="   1" pdb=" N   ILE A  77 "
       model="   1" pdb=" CA  ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.458  1.515 -0.057 1.90e-02 2.77e+03 9.05e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       66.25 -    80.15: 2
       80.15 -    94.05: 7
       94.05 -   107.96: 584
      107.96 -   121.86: 3059
      121.86 -   135.76: 427
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   1" pdb=" N   THR A  82 "
        model="   1" pdb=" CA  THR A  82 "
        model="   1" pdb=" HA  THR A  82 "
      ideal   model   delta    sigma   weight residual
     110.00   66.25   43.75 3.00e+00 1.11e-01 2.13e+02
  angle model="   1" pdb=" C   ILE A  78 "
        model="   1" pdb=" CA  ILE A  78 "
        model="   1" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     109.00   74.53   34.47 3.00e+00 1.11e-01 1.32e+02
  angle model="   1" pdb=" C   LYS A  79 "
        model="   1" pdb=" CA  LYS A  79 "
        model="   1" pdb=" CB  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     110.10   92.98   17.12 1.90e+00 2.77e-01 8.12e+01
  angle model="   1" pdb=" CA  ILE A  51 "
        model="   1" pdb=" C   ILE A  51 "
        model="   1" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  129.07  -12.17 1.50e+00 4.44e-01 6.59e+01
  angle model="   1" pdb=" N   LEU A  70 "
        model="   1" pdb=" CA  LEU A  70 "
        model="   1" pdb=" CB  LEU A  70 "
      ideal   model   delta    sigma   weight residual
     110.50   97.00   13.50 1.70e+00 3.46e-01 6.31e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.19: 915
       18.19 -    36.37: 70
       36.37 -    54.56: 28
       54.56 -    72.75: 6
       72.75 -    90.93: 2
  Dihedral angle restraints: 1021
    sinusoidal: 562
      harmonic: 459
  Sorted by residual:
  dihedral model="   1" pdb=" C   THR A  82 "
           model="   1" pdb=" N   THR A  82 "
           model="   1" pdb=" CA  THR A  82 "
           model="   1" pdb=" CB  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -175.19   53.19     0      2.50e+00 1.60e-01 4.53e+02
  dihedral model="   1" pdb=" N   THR A  82 "
           model="   1" pdb=" C   THR A  82 "
           model="   1" pdb=" CA  THR A  82 "
           model="   1" pdb=" CB  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  175.32  -51.92     0      2.50e+00 1.60e-01 4.31e+02
  dihedral model="   1" pdb=" CA  THR A  92 "
           model="   1" pdb=" C   THR A  92 "
           model="   1" pdb=" N   LEU A  93 "
           model="   1" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -89.07  -90.93     0      5.00e+00 4.00e-02 3.31e+02
  ... (remaining 1018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.109: 166
       1.109 -    2.217: 0
       2.217 -    3.324: 2
       3.324 -    4.432: 2
       4.4
  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.19
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CB  PRO A  52 "
        model="   3" pdb=" CB  LYS A  79 "
        model="   3" pdb=" CB  THR A  92 "
        model="   3" pdb=" CB  SER A  97 "
        model="   3" pdb=" CB  ILE A 122 "
        model="   3" pdb=" CB  GLU A 123 "
        model="   3" pdb=" CB  VAL A 126 "
        model="   3" pdb=" CB  ARG A 127 "
        model="   3" pdb=" CB  HIS A 139 "
  Number of C-beta restraints generated:  244

  Time building geometry restraints manager: 1.32 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

32 -    5.540: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  LYS A  79 "
            model="   1" pdb=" N   LYS A  79 "
            model="   1" pdb=" C   LYS A  79 "
            model="   1" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.03    5.54 2.00e-01 2.50e+01 7.67e+02
  chirality model="   1" pdb=" CB  ILE A  78 "
            model="   1" pdb=" CA  ILE A  78 "
            model="   1" pdb=" CG1 ILE A  78 "
            model="   1" pdb=" CG2 ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.59    5.23 2.00e-01 2.50e+01 6.85e+02
  chirality model="   1" pdb=" CB  THR A  82 "
            model="   1" pdb=" CA  THR A  82 "
            model="   1" pdb=" OG1 THR A  82 "
            model="   1" pdb=" CG2 THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.52    5.08 2.00e-01 2.50e+01 6.44e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  81 "   -0.256 2.00e-02 2.50e+03   1.07e-01 3.44e+02
        model="   1" pdb=" CG  TYR A  81 "    0.015 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  81 "    0.082 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  81 "    0.036 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  81 "    0.032 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  81 "   -0.036 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  81 "   -0.124 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  81 "    0.187 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  81 "    0.053 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  81 "   -0.053 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  81 "    0.074 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  PHE A  15 "   -0.215 2.00e-02 2.50e+03   8.71e-02 2.28e+02
        model="   1" pdb=" CG  PHE A  15 "    0.017 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 PHE A  15 "    0.045 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 PHE A  15 "    0.059 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 PHE A  15 "    0.013 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  PHE A  15 "   -0.045 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 PHE A  15 "    0.084 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 PHE A  15 "    0.125 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 PHE A  15 "    0.031 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 PHE A  15 "   -0.003 2.00e-02 2.50e+03
        model="   1" pdb=" HZ  PHE A  15 "   -0.115 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  91 "    0.168 2.00e-02 2.50e+03   7.24e-02 1.57e+02
        model="   1" pdb=" CG  TYR A  91 "   -0.032 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  91 "   -0.031 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  91 "   -0.041 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  91 "   -0.029 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  91 "   -0.020 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  91 "    0.147 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  91 "   -0.031 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  91 "   -0.062 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  91 "   -0.053 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  91 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.25: 271
        2.25 -     2.84: 4896
        2.84 -     3.43: 6048
        3.43 -     4.01: 7915
        4.01 -     4.60: 11792
  Nonbonded interactions: 30922
  Sorted by model distance:
  nonbonded model="   1" pdb=" H   ILE A  78 "
            model="   1" pdb=" HG3 LYS A  79 "
     model   vdw
     1.666 2.270
  nonbonded model="   1" pdb=" O   TYR A  89 "
            model="   1" pdb=" HG  SER A  90 "
     model   vdw
     1.760 1.850
  nonbonded model="   1" pdb=" HA  LYS A  79 "
            model="   1" pdb=" HB  THR A  82 "
     model   vdw
     1.762 2.440
  nonbonded model="   1" pdb=" HE2 PHE A  15 "
            model="   1" pdb="HD11 ILE A  86 "
     model   vdw
     1.775 2.270
  nonbonded model="   1" pdb=" O   SER A  76 "
            model="   1" pdb=" HH  TYR A  81 "
     model   vdw
     1.792 1.850
  ... (remaining 30917 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 68
        1.23 -     1.43: 410
        1.43 -     1.62: 654
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   3" pdb=" N   THR A  92 "
       model="   3" pdb=" CA  THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.458  1.337  0.121 1.90e-02 2.77e+03 4.06e+01
  bond model="   3" pdb=" CA  TYR A  91 "
       model="   3" pdb=" C   TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.525  1.402  0.123 2.10e-02 2.27e+03 3.41e+01
  bond model="   3" pdb=" N   GLY A  80 "
       model="   3" pdb=" CA  GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.451  1.519 -0.068 1.60e-02 3.91e+03 1.80e+01
  bond model="   3" pdb=" C   TYR A  91 "
       model="   3" pdb=" N   THR A  92 "
    ideal  model  delta    sigma   weight residual
    1.329  1.270  0.059 1.40e-02 5.10e+03 1.79e+01
  bond model="   3" pdb=" C   VAL A 126 "
       model="   3" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.274  0.055 1.40e-02 5.10e+03 1.55e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       87.87 -    97.13: 13
       97.13 -   106.40: 217
      106.40 -   115.67: 2713
      115.67 -   124.94: 1025
      124.94 -   134.21: 111
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   3" pdb=" CA  THR A  92 "
        model="   3" pdb=" CB  THR A  92 "
        model="   3" pdb=" CG2 THR A  92 "
      ideal   model   delta    sigma   weight residual
     110.50  133.16  -22.66 1.70e+00 3.46e-01 1.78e+02
  angle model="   3" pdb=" OG1 THR A  92 "
        model="   3" pdb=" CB  THR A  92 "
        model="   3" pdb=" CG2 THR A  92 "
      ideal   model   delta    sigma   weight residual
     109.30   88.29   21.01 2.00e+00 2.50e-01 1.10e+02
  angle model="   3" pdb=" CA  VAL A 126 "
        model="   3" pdb=" CB  VAL A 126 "
        model="   3" pdb=" CG2 VAL A 126 "
      ideal   model   delta    sigma   weight residual
     110.40  125.57  -15.17 1.70e+00 3.46e-01 7.96e+01
  angle model="   3" pdb=" OG1 THR A  92 "
        model="   3" pdb=" CB  THR A  92 "
        model="   3" pdb=" HB  THR A  92 "
      ideal   model   delta    sigma   weight residual
     109.00  134.21  -25.21 3.00e+00 1.11e-01 7.06e+01
  angle model="   3" pdb=" C   VAL A 126 "
        model="   3" pdb=" CA  VAL A 126 "
        model="   3" pdb=" CB  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     111.40  127.21  -15.81 1.90e+00 2.77e-01 6.93e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.48: 951
       24.48 -    48.97: 43
       48.97 -    73.45: 10
       73.45 -    97.93: 4
       97.93 -   122.42: 5
  Dihedral angle restraints: 1013
    sinusoidal: 562
      harmonic: 451
  Sorted by residual:
  dihedral model="   3" pdb=" CA  TYR A  89 "
           model="   3" pdb=" C   TYR A  89 "
           model="   3" pdb=" N   SER A  90 "
           model="   3" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -57.58 -122.42     0      5.00e+00 4.00e-02 5.99e+02
  dihedral model="   3" pdb=" CA  SER A  90 "
           model="   3" pdb=" C   SER A  90 "
           model="   3" pdb=" N   TYR A  91 "
           model="   3" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -59.51 -120.49     0      5.00e+00 4.00e-02 5.81e+02
  dihedral model="   3" pdb=" CA  LYS A 125 "
           model="   3" pdb=" C   LYS A 125 "
           model="   3" pdb=" N   VAL A 126 "
           model="   3" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   68.57  111.43     0      5.00e+00 4.00e-02 4.97e+02
  ... (remaining 1010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.032: 165
       1.032 -    2.064: 0
       2.064 -    3.095: 0
       3.095 -    4.127: 0
       4.127 -    5.158: 11
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   3" pdb=" CB  ILE A 131 "
            model="   3" pdb=" CA  ILE A 131 "
            model="   3" pdb=" CG1 ILE A 131 "
            model="   3" pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.51    5.16 2.00e-01 2.50e+01 6.65e+02
  chirality model="   3" pdb=" CA  PRO A  52 "
            model="   3" pdb=" N   PRO A  52 "
            model="   3" pdb=" C   PRO A  52 "
            model="   3" pdb=" CB  PRO A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72   -2.41    5.12 2.00e-01 2.50e+01 6.57e+02
  chirality model="   3" pdb=" CA  VAL A 126 "
            model="   3" pdb=" N   VAL A 126 "
            model="   3" pdb=" C   VAL A 126 "
            model="   3" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44   -2.64    5.08 2.00e-01 2.50e+01 6.45e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  12 "   -0.115 2.00e-02 2.50e+03   5.18e-02 8.06e+01
        model="   3" pdb=" CG  TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  12 "    0.018 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  12 "   -0.106 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  12 "    0.052 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  12 "    0.047 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  91 "   -0.105 2.00e-02 2.50e+03   4.26e-02 5.44e+01
        model="   3" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  91 "    0.025 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  91 "    0.024 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  91 "    0.007 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  91 "   -0.018 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  91 "   -0.057 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  91 "    0.056 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  91 "    0.051 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  91 "    0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A 111 "    0.099 2.00e-02 2.50e+03   4.02e-02 4.84e+01
        model="   3" pdb=" CG  TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A 111 "    0.072 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A 111 "   -0.040 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A 111 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 120
        2.12 -     2.74: 3770
        2.74 -     3.36: 6536
        3.36 -     3.98: 7819
        3.98 -     4.60: 11790
  Nonbonded interactions: 30035
  Sorted by model distance:
  nonbonded model="   3" pdb=" HA  LYS A  79 "
            model="   3" pdb="HD12 LEU A  93 "
     model   vdw
     1.500 2.440
  nonbonded model="   3" pdb=" HB  THR A  92 "
            model="   3" pdb=" HB2 LEU A  93 "
     model   vdw
     1.646 2.440
  nonbonded model="   3" pdb=" OD1 ASP A  74 "
            model="   3" pdb=" HG  SER A  76 "
     model   vdw
     1.765 1.850
  nonbonded model="   3" pdb=" O   ARG A 127 "
            model="   3" pdb=" HG  SER A 130 "
     model   vdw
     1.771 1.850
  nonbonded model="   3" pdb=" HG1 THR A  92 "
            model="   3" pdb="HG21 THR A  92 "
     model   vdw
     1.781 2.270
  ... (remaining 30030 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   3" pdb=" CB  ILE A  51 "
        model="   3" pdb=" CB  ASP A  74 "
        model="   3" pdb=" CB  ILE A  78 "
        model="   3" pdb=" CB  LYS A  79 "
        model="   3" pdb=" CB  TYR A  89 "
        model="   3" pdb=" CB  TYR A  91 "
        model="   3" pdb=" CB  THR A  92 "
        model="   3" pdb=" CB  SER A  98 "
        model="   3" pdb=" CB  ALA A 124 "
  Number of C-beta restraints generated:  246

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 56
        1.23 -     1.43: 420
        1.43 -     1.62: 654
        1.62 -     1.82: 6
  Bond restraints: 2242
  Sorted by residual:
  bond model="   3" pdb=" N   LEU A 132 "
       model="   3" pdb=" CA  LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.458  1.600 -0.142 1.90e-02 2.77e+03 5.60e+01
  bond model="   3" pdb=" CA  ARG A 127 "
       model="   3" pdb=" C   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.525  1.640 -0.115 2.10e-02 2.27e+03 3.02e+01
  bond model="   3" pdb=" N   ARG A 129 "
       model="   3" pdb=" CA  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.458  1.555 -0.097 1.90e-02 2.77e+03 2.61e+01
  bond model="   3" pdb=" C   ALA A 124 "
       model="   3" pdb=" N   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.329  1.261  0.068 1.40e-02 5.10e+03 2.37e+01
  bond model="   3" pdb=" C   VAL A 126 "
       model="   3" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.264  0.065 1.40e-02 5.10e+03 2.15e+01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       79.83 -    92.34: 8
       92.34 -   104.85: 112
      104.85 -   117.36: 2926
      117.36 -   129.87: 1018
      129.87 -   142.38: 15
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   3" pdb=" C   ARG A 127 "
        model="   3" pdb=" CA  ARG A 127 "
        model="   3" pdb=" CB  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     110.10  141.13  -31.03 1.90e+00 2.77e-01 2.67e+02
  angle model="   3" pdb=" N   VAL A 126 "
        model="   3" pdb=" CA  VAL A 126 "
        model="   3" pdb=" CB  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     111.50   88.49   23.01 1.70e+00 3.46e-01 1.83e+02
  angle model="   3" pdb=" C   VAL A 126 "
        model="   3" pdb=" CA  VAL A 126 "
        model="   3" pdb=" CB  VAL A 126 "
      ideal   model   delta    sigma   weight residual
     111.40   88.72   22.68 1.90e+00 2.77e-01 1.43e+02
  angle model="   3" pdb=" C   VAL A 126 "
        model="   3" pdb=" N   ARG A 127 "
        model="   3" pdb=" CA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     121.70  100.25   21.45 1.80e+00 3.09e-01 1.42e+02
  angle model="   3" pdb=" N   ARG A 127 "
        model="   3" pdb=" CA  ARG A 127 "
        model="   3" pdb=" HA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     110.00  142.38  -32.38 3.00e+00 1.11e-01 1.17e+02
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.61: 927
       24.61 -    49.21: 67
       49.21 -    73.82: 11
       73.82 -    98.42: 8
       98.42 -   123.03: 2
  Dihedral angle restraints: 1015
    sinusoidal: 562
      harmonic: 453
  Sorted by residual:
  dihedral model="   3" pdb=" CA  GLY A  96 "
           model="   3" pdb=" C   GLY A  96 "
           model="   3" pdb=" N   SER A  97 "
           model="   3" pdb=" CA  SER A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   56.97  123.03     0      5.00e+00 4.00e-02 6.05e+02
  dihedral model="   3" pdb=" CA  VAL A 126 "
           model="   3" pdb=" C   VAL A 126 "
           model="   3" pdb=" N   ARG A 127 "
           model="   3" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   57.13  122.87     0      5.00e+00 4.00e-02 6.04e+02
  dihedral model="   3" pdb=" CA  ARG A 127 "
           model="   3" pdb=" C   ARG A 127 "
           model="   3" pdb=" N   MET A 128 "
           model="   3" pdb=" CA  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   81.65   98.35     0      5.00e+00 4.00e-02 3.87e+02
  ... (remaining 1012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    1.166: 164
       1.166 -    2.331: 2
       2.331 -    3.496: 1
       3.496 -    4.661: 1
       4.661 -    5.826: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   3" pdb=" CA  LYS A  79 "
            model="   3" pdb=" N   LYS A  79 "
            model="   3" pdb=" C   LYS A  79 "
            model="   3" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -3.32    5.83 2.00e-01 2.50e+01 8.49e+02
  chirality model="   3" pdb=" CB  ILE A  77 "
            model="   3" pdb=" CA  ILE A  77 "
            model="   3" pdb=" CG1 ILE A  77 "
            model="   3" pdb=" CG2 ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64   -2.68    5.33 2.00e-01 2.50e+01 7.10e+02
  chirality model="   3" pdb=" CA  TYR A  91 "
            model="   3" pdb=" N   TYR A  91 "
            model="   3" pdb=" C   TYR A  91 "
            model="   3" pdb=" CB  TYR A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.51    5.02 2.00e-01 2.50e+01 6.29e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  91 "    0.611 2.00e-02 2.50e+03   2.61e-01 2.05e+03
        model="   3" pdb=" CG  TYR A  91 "   -0.011 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  91 "   -0.175 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  91 "   -0.087 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  91 "   -0.030 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  91 "   -0.109 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  91 "    0.445 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  91 "   -0.374 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  91 "   -0.122 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  91 "    0.042 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  91 "   -0.199 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A  89 "    0.123 2.00e-02 2.50e+03   5.04e-02 7.61e+01
        model="   3" pdb=" CG  TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A  89 "   -0.026 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A  89 "   -0.027 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A  89 "   -0.013 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A  89 "    0.009 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A  89 "    0.089 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A  89 "   -0.047 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A  89 "   -0.051 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A  89 "   -0.020 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A  89 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   3" pdb=" CB  TYR A 111 "   -0.074 2.00e-02 2.50e+03   3.02e-02 2.73e+01
        model="   3" pdb=" CG  TYR A 111 "    0.024 2.00e-02 2.50e+03
        model="   3" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   3" pdb=" CD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   3" pdb=" CE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   3" pdb=" CE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   3" pdb=" CZ  TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   3" pdb=" OH  TYR A 111 "   -0.046 2.00e-02 2.50e+03
        model="   3" pdb=" HD1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   3" pdb=" HD2 TYR A 111 "    0.037 2.00e-02 2.50e+03
        model="   3" pdb=" HE1 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   3" pdb=" HE2 TYR A 111 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 114
        2.11 -     2.73: 3731
        2.73 -     3.36: 6516
        3.36 -     3.98: 7790
        3.98 -     4.60: 11583
  Nonbonded interactions: 29734
  Sorted by model distance:
  nonbonded model="   3" pdb=" HB2 ARG A 127 "
            model="   3" pdb=" H   ARG A 129 "
     model   vdw
     1.491 2.270
  nonbonded model="   3" pdb=" HA  ARG A 127 "
            model="   3" pdb=" H   ARG A 129 "
     model   vdw
     1.607 2.270
  nonbonded model="   3" pdb=" HA  SER A  76 "
            model="   3" pdb=" HB2 LYS A  79 "
     model   vdw
     1.608 2.440
  nonbonded model="   3" pdb=" H   VAL A 126 "
            model="   3" pdb="HG23 VAL A 126 "
     model   vdw
     1.659 2.270
  nonbonded model="   3" pdb="HG21 ILE A  78 "
            model="   3" pdb=" H   GLY A  94 "
     model   vdw
     1.662 2.270
  ... (remaining 29729 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        model="   1" pdb=" CB  ILE A  51 "
        model="   1" pdb=" CB  ILE A  78 "
        model="   1" pdb=" CB  LYS A  79 "
        model="   1" pdb=" CB  ASP A  88 "
        model="   1" pdb=" CB  SER A  97 "
        model="   1" pdb=" CB  GLU A 120 "
        model="   1" pdb=" CB  GLU A 123 "
        model="   1" pdb=" CB  ALA A 124 "
  Number of C-beta restraints generated:  248

  Time building geometry restraints manager: 1.27 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1105
        1.04 -     1.25: 137
        1.25 -     1.45: 366
        1.45 -     1.65: 618
        1.65 -     1.86: 15
  Bond restraints: 2241
  Sorted by residual:
  bond model="   1" pdb=" N   LYS A  79 "
       model="   1" pdb=" CA  LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.458  1.745 -0.287 1.90e-02 2.77e+03 2.28e+02
  bond model="   1" pdb=" CB  LEU A  93 "
       model="   1" pdb=" CG  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.789 -0.259 2.00e-02 2.50e+03 1.67e+02
  bond model="   1" pdb=" N   ARG A 127 "
       model="   1" pdb=" CA  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.458  1.654 -0.196 1.90e-02 2.77e+03 1.06e+02
  bond model="   1" pdb=" CA  LEU A  93 "
       model="   1" pdb=" CB  LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.326  0.204 2.00e-02 2.50e+03 1.04e+02
  bond model="   1" pdb=" N   ILE A 122 "
       model="   1" pdb=" CA  ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.652 -0.194 1.90e-02 2.77e+03 1.04e+02
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       34.60 -    57.41: 2
       57.41 -    80.23: 7
       80.23 -   103.04: 87
      103.04 -   125.86: 3855
      125.86 -   148.67: 127
  Bond angle restraints: 4078
  Sorted by residual:
  angle model="   1" pdb=" O   ALA A 124 "
        model="   1" pdb=" C   ALA A 124 "
        model="   1" pdb=" N   LYS A 125 "
      ideal   model   delta    sigma   weight residual
     123.00   65.56   57.44 1.60e+00 3.91e-01 1.29e+03
  angle model="   1" pdb=" OG1 THR A  92 "
        model="   1" pdb=" CB  THR A  92 "
        model="   1" pdb=" CG2 THR A  92 "
      ideal   model   delta    sigma   weight residual
     109.30   41.87   67.43 2.00e+00 2.50e-01 1.14e+03
  angle model="   1" pdb=" N   ARG A 127 "
        model="   1" pdb=" CA  ARG A 127 "
        model="   1" pdb=" HA  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     110.00   34.60   75.40 3.00e+00 1.11e-01 6.32e+02
  angle model="   1" pdb=" CA  ALA A 124 "
        model="   1" pdb=" C   ALA A 124 "
        model="   1" pdb=" O   ALA A 124 "
      ideal   model   delta    sigma   weight residual
     120.80   82.78   38.02 1.70e+00 3.46e-01 5.00e+02
  angle model="   1" pdb=" CD1 LEU A  93 "
        model="   1" pdb=" CG  LEU A  93 "
        model="   1" pdb=" CD2 LEU A  93 "
      ideal   model   delta    sigma   weight residual
     110.80   69.24   41.56 2.20e+00 2.07e-01 3.57e+02
  ... (remaining 4073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.90: 912
       23.90 -    47.80: 72
       47.80 -    71.70: 24
       71.70 -    95.60: 4
       95.60 -   119.50: 4
  Dihedral angle restraints: 1016
    sinusoidal: 561
      harmonic: 455
  Sorted by residual:
  dihedral model="   1" pdb=" CA  VAL A 126 "
           model="   1" pdb=" C   VAL A 126 "
           model="   1" pdb=" N   ARG A 127 "
           model="   1" pdb=" CA  ARG A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   60.50  119.50     0      5.00e+00 4.00e-02 5.71e+02
  dihedral model="   1" pdb=" CA  TYR A  89 "
           model="   1" pdb=" C   TYR A  89 "
           model="   1" pdb=" N   SER A  90 "
           model="   1" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -62.13 -117.87     0      5.00e+00 4.00e-02 5.56e+02
  dihedral model="   1" pdb=" CA  THR A  92 "
           model="   1" pdb=" C   THR A  92 "
           model="   1" pdb=" N   LEU A  93 "
           model="   1" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   66.91  113.09     0      5.00e+00 4.00e-02 5.12e+02
  ... (remaining 1013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    1.396: 162
       1.396 -    2.791: 3
       2.791 -    4.186: 6
       4.186 -    5.580: 4
       5.580 -    6.975: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  LYS A  79 "
            model="   1" pdb=" N   LYS A  79 "
            model="   1" pdb=" C   LYS A  79 "
            model="   1" pdb=" CB  LYS A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -4.46    6.98 2.00e-01 2.50e+01 1.22e+03
  chirality model="   1" pdb=" CA  GLU A 123 "
            model="   1" pdb=" N   GLU A 123 "
            model="   1" pdb=" C   GLU A 123 "
            model="   1" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.77    5.28 2.00e-01 2.50e+01 6.96e+02
  chirality model="   1" pdb=" CA  ALA A 124 "
            model="   1" pdb=" N   ALA A 124 "
            model="   1" pdb=" C   ALA A 124 "
            model="   1" pdb=" CB  ALA A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48   -2.70    5.19 2.00e-01 2.50e+01 6.72e+02
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  89 "   -1.626 2.00e-02 2.50e+03   5.72e-01 9.82e+03
        model="   1" pdb=" CG  TYR A  89 "   -0.086 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  89 "    0.259 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  89 "    0.311 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  89 "    0.111 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  89 "    0.071 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  89 "   -0.167 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  89 "   -0.429 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  89 "    0.569 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  89 "    0.720 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  89 "    0.196 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  89 "    0.070 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  81 "    0.224 2.00e-02 2.50e+03   1.78e-01 9.55e+02
        model="   1" pdb=" CG  TYR A  81 "    0.069 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  81 "   -0.132 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  81 "    0.017 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  81 "    0.105 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  81 "   -0.039 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  81 "    0.063 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  81 "   -0.026 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  81 "   -0.438 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  81 "    0.282 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  81 "   -0.145 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  PHE A  67 "    0.081 2.00e-02 2.50e+03   1.32e-01 5.19e+02
        model="   1" pdb=" CG  PHE A  67 "    0.019 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 PHE A  67 "   -0.092 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 PHE A  67 "    0.045 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 PHE A  67 "    0.080 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 PHE A  67 "   -0.056 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  PHE A  67 "   -0.003 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 PHE A  67 "   -0.277 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 PHE A  67 "    0.128 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 PHE A  67 "    0.252 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 PHE A  67 "   -0.156 2.00e-02 2.50e+03
        model="   1" pdb=" HZ  PHE A  67 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.16 -     1.85: 35
        1.85 -     2.54: 2029
        2.54 -     3.22: 7224
        3.22 -     3.91: 9099
        3.91 -     4.60: 13721
  Nonbonded interactions: 32108
  Sorted by model distance:
  nonbonded model="   1" pdb=" H   LEU A  93 "
            model="   1" pdb=" HA  SER A  97 "
     model   vdw
     1.159 2.270
  nonbonded model="   1" pdb=" OG1 THR A  92 "
            model="   1" pdb="HG22 THR A  92 "
     model   vdw
     1.201 2.096
  nonbonded model="   1" pdb=" HA  THR A  92 "
            model="   1" pdb=" HB  THR A  92 "
     model   vdw
     1.250 1.952
  nonbonded model="   1" pdb=" H   THR A  92 "
            model="   1" pdb=" HB2 LEU A  99 "
     model   vdw
     1.261 2.270
  nonbonded model="   1" pdb="HD13 LEU A  93 "
            model="   1" pdb="HD22 LEU A  93 "
     model   vdw
     1.453 2.440
  ... (remaining 32103 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 125  LYS  N
   A 125  LYS  CA          1.46     1.66    -0.20  1.90e-02  1.09e+02  10.4*sigma
   A 124  ALA  C
   A 125  LYS  N           1.33     1.43    -0.10  1.40e-02  5.20e+01   7.2*sigma
   A 124  ALA  CA
   A 124  ALA  C           1.52     1.64    -0.12  2.10e-02  3.26e+01   5.7*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.25     0.08  1.40e-02  2.91e+01   5.4*sigma
   A 123  GLU  CA
   A 123  GLU  CB          1.53     1.63    -0.10  2.00e-02  2.39e+01   4.9*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.198 (Z= 10.423)
  Mean delta:    0.018 (Z=  0.948)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   148.91   -27.21  1.80e+00  2.28e+02  15.1*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   134.60   -24.20  1.70e+00  2.03e+02  14.2*sigma
   A 129  ARG  C
   A 129  ARG  CA
   A 129  ARG  CB        110.10   135.19   -25.09  1.90e+00  1.74e+02  13.2*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70    98.43    23.27  1.80e+00  1.67e+02  12.9*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20    97.88    18.32  2.00e+00  8.39e+01   9.2*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N         116.20    99.25    16.95  2.00e+00  7.19e+01   8.5*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   106.67    15.03  1.80e+00  6.97e+01   8.3*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   107.40    14.30  1.80e+00  6.31e+01   7.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   100.33    15.87  2.00e+00  6.30e+01   7.9*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  C         111.00   132.98   -21.98  2.80e+00  6.16e+01   7.9*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   127.90   -11.00  1.50e+00  5.37e+01   7.3*sigma
   A 116  ASP  C
   A 116  ASP  CA
   A 116  ASP  CB        110.10   123.49   -13.39  1.90e+00  4.97e+01   7.0*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10    94.39    14.71  2.20e+00  4.47e+01   6.7*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 119  LEU  O         120.80   131.50   -10.70  1.70e+00  3.96e+01   6.3*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   132.71   -11.01  1.80e+00  3.74e+01   6.1*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   123.81   -12.21  2.00e+00  3.73e+01   6.1*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.62    -6.02  1.00e+00  3.63e+01   6.0*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80    97.64    13.16  2.20e+00  3.58e+01   6.0*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   120.53   -10.13  1.70e+00  3.55e+01   6.0*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00   127.61   -16.61  2.80e+00  3.52e+01   5.9*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   104.40    11.80  2.00e+00  3.48e+01   5.9*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O         120.80   130.82   -10.02  1.70e+00  3.48e+01   5.9*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   131.94   -10.24  1.80e+00  3.24e+01   5.7*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   121.15    -9.65  1.70e+00  3.22e+01   5.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.89   -10.19  1.80e+00  3.21e+01   5.7*sigma
   A 133  GLU  C
   A 133  GLU  CA
   A 133  GLU  CB        110.10   120.82   -10.72  1.90e+00  3.18e+01   5.6*sigma
   A  70  LEU  N
   A  70  LEU  CA
   A  70  LEU  CB        110.50   101.11     9.39  1.70e+00  3.05e+01   5.5*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   119.65    -9.15  1.70e+00  2.90e+01   5.4*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   120.21   -10.11  1.90e+00  2.83e+01   5.3*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG1       110.40   119.42    -9.02  1.70e+00  2.82e+01   5.3*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   131.14    -9.44  1.80e+00  2.75e+01   5.2*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   100.14     9.96  1.90e+00  2.75e+01   5.2*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   131.09    -9.39  1.80e+00  2.72e+01   5.2*sigma
   A 123  GLU  O
   A 123  GLU  C
   A 124  ALA  N         123.00   131.22    -8.22  1.60e+00  2.64e+01   5.1*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   117.71    -5.11  1.00e+00  2.61e+01   5.1*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   121.81   -10.21  2.00e+00  2.61e+01   5.1*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   129.48    -8.68  1.70e+00  2.61e+01   5.1*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.57     5.03  1.00e+00  2.53e+01   5.0*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   130.66    -8.96  1.80e+00  2.48e+01   5.0*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    97.09    13.91  2.80e+00  2.47e+01   5.0*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   130.56    -8.86  1.80e+00  2.42e+01   4.9*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   128.98    -8.18  1.70e+00  2.32e+01   4.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N         116.20   125.49    -9.29  2.00e+00  2.16e+01   4.6*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   117.22    -4.62  1.00e+00  2.13e+01   4.6*sigma
   A  97  SER  CA
   A  97  SER  C
   A  97  SER  O         120.80   128.61    -7.81  1.70e+00  2.11e+01   4.6*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG2       110.50   118.29    -7.79  1.70e+00  2.10e+01   4.6*sigma
   A 114  PRO  N
   A 114  PRO  CA
   A 114  PRO  CB        103.00   108.04    -5.04  1.10e+00  2.10e+01   4.6*sigma
   A 124  ALA  O
   A 124  ALA  C
   A 125  LYS  N         123.00   115.79     7.21  1.60e+00  2.03e+01   4.5*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.03    -4.43  1.00e+00  1.97e+01   4.4*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   124.89    -8.69  2.00e+00  1.89e+01   4.3*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  93  LEU  O         120.80   113.55     7.25  1.70e+00  1.82e+01   4.3*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N         116.20   107.69     8.51  2.00e+00  1.81e+01   4.3*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   129.33    -7.63  1.80e+00  1.80e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.73e+01   4.2*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   122.56   -11.56  2.80e+00  1.70e+01   4.1*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   116.71    -4.11  1.00e+00  1.69e+01   4.1*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  C         111.00    99.59    11.41  2.80e+00  1.66e+01   4.1*sigma
   A 125  LYS  O
   A 125  LYS  C
   A 126  VAL  N         123.00   129.51    -6.51  1.60e+00  1.65e+01   4.1*sigma
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        121.70   128.92    -7.22  1.80e+00  1.61e+01   4.0*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   117.72    -7.62  1.90e+00  1.61e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   27.207 (Z= 15.115)
  Mean delta:    3.312 (Z=  1.764)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    57.19   122.81  5.00e+00  6.03e+02  24.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    92.81    87.19  5.00e+00  3.04e+02  17.4*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00    94.12    85.88  5.00e+00  2.95e+02  17.2*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   -95.60   -84.40  5.00e+00  2.85e+02  16.9*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -100.17   -79.83  5.00e+00  2.55e+02  16.0*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   102.54    77.46  5.00e+00  2.40e+02  15.5*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   116.13    63.87  5.00e+00  1.63e+02  12.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -118.31   -61.69  5.00e+00  1.52e+02  12.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -124.96   -55.04  5.00e+00  1.21e+02  11.0*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -125.25   -54.75  5.00e+00  1.20e+02  11.0*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   128.14    51.86  5.00e+00  1.08e+02  10.4*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -128.86   -51.14  5.00e+00  1.05e+02  10.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -134.49   -45.51  5.00e+00  8.28e+01   9.1*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   139.70    40.30  5.00e+00  6.50e+01   8.1*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -141.63   -38.37  5.00e+00  5.89e+01   7.7*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00   143.66    36.34  5.00e+00  5.28e+01   7.3*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -145.51   -34.49  5.00e+00  4.76e+01   6.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00  -145.75   -34.25  5.00e+00  4.69e+01   6.9*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00  -147.51   -32.49  5.00e+00  4.22e+01   6.5*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -148.10   -31.90  5.00e+00  4.07e+01   6.4*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00  -150.15   -29.85  5.00e+00  3.56e+01   6.0*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   150.32    29.68  5.00e+00  3.52e+01   5.9*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA          0.00    27.31   -27.31  5.00e+00  2.98e+01   5.5*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   153.31    26.69  5.00e+00  2.85e+01   5.3*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -153.80   -26.20  5.00e+00  2.74e+01   5.2*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -154.75   -25.25  5.00e+00  2.55e+01   5.0*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   157.30    22.70  5.00e+00  2.06e+01   4.5*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00  -158.02   -21.98  5.00e+00  1.93e+01   4.4*sigma

  Min. delta:    0.008
  Max. delta:  122.809
  Mean delta:   19.522

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.53     5.04  2.00e-01  6.35e+02  25.2*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.25     4.90  2.00e-01  5.99e+02  24.5*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -2.41     4.84  2.00e-01  5.86e+02  24.2*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.30     4.74  2.00e-01  5.62e+02  23.7*sigma
   A 119  LEU  CA
   A 119  LEU  N
   A 119  LEU  C
   A 119  LEU  CB          2.51    -2.22     4.73  2.00e-01  5.58e+02  23.6*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.21     4.72  2.00e-01  5.58e+02  23.6*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.01     4.52  2.00e-01  5.11e+02  22.6*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -1.99     4.50  2.00e-01  5.06e+02  22.5*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -1.98     4.49  2.00e-01  5.03e+02  22.4*sigma
   A 125  LYS  CA
   A 125  LYS  N
   A 125  LYS  C
   A 125  LYS  CB          2.51    -0.76     3.27  2.00e-01  2.68e+02  16.4*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.73     3.16  2.00e-01  2.50e+02  15.8*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.33     1.19  2.00e-01  3.51e+01   5.9*sigma
   A 126  VAL  CB
   A 126  VAL  CA
   A 126  VAL  CG1
   A 126  VAL  CG2        -2.63    -1.74    -0.89  2.00e-01  1.96e+01   4.4*sigma
   A 129  ARG  CA
   A 129  ARG  N
   A 129  ARG  C
   A 129  ARG  CB          2.51     1.71     0.80  2.00e-01  1.61e+01   4.0*sigma

  Min. delta:    0.001
  Max. delta:    5.042
  Mean delta:    1.141

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.056       0.102       62.46   5.1*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.052       0.092       53.23   4.6*sigma
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.048       0.092       46.68   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.077
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    4" pdbres="HIS A  43  conformer  : HE2, HD1 
    4" pdbres="HIS A 134  conformer  : HE2, HD1 
    4" pdbres="HIS A 135  conformer  : HE2, HD1 
    4" pdbres="HIS A 136  conformer  : HE2, HD1 
    4" pdbres="HIS A 137  conformer  : HE2, HD1 
    4" pdbres="HIS A 138  conformer  : HE2, HD1 
    4" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 125  LYS  H  , Angle CA-N-H, observed: 101.351, delta from target: 12.649
   A 116  ASP  HA , Angle CB-CA-HA, observed: 95.549, delta from target: 13.451
   A  79  LYS  HA , Angle N-CA-HA, observed: 96.422, delta from target: 13.578
   A  95  ASP  HA , Angle C-CA-HA, observed: 95.363, delta from target: 13.637
   A 125  LYS  HA , Angle CB-CA-HA, observed: 122.715, delta from target: -13.715
   A 123  GLU  HA , Angle N-CA-HA, observed: 95.998, delta from target: 14.002
   A 125  LYS  H  , Angle C-N-H, observed: 109.742, delta from target: 14.558
   A 126  VAL  HA , Angle CB-CA-HA, observed: 92.893, delta from target: 16.107
   A 123  GLU  HA , Angle C-CA-HA, observed: 92.561, delta from target: 16.439
   A  92  THR  HA , Angle CB-CA-HA, observed: 125.672, delta from target: -16.672
   A  78  ILE  HB , Angle CA-CB-HB, observed: 91.240, delta from target: 17.760
   A 127  ARG  HA , Angle C-CA-HA, observed: 89.566, delta from target: 19.434
   A 123  GLU  HA , Angle CB-CA-HA, observed: 128.435, delta from target: -19.435
   A 125  LYS  HA , Angle N-CA-HA, observed: 90.065, delta from target: 19.935
   A  51  ILE  HA , Angle CB-CA-HA, observed: 88.896, delta from target: 20.104
   A 129  ARG  HA , Angle N-CA-HA, observed: 130.715, delta from target: -20.715
   A 126  VAL  HB , Angle CG1-CB-HB, observed: 129.517, delta from target: -21.517
   A 129  ARG  HA , Angle CB-CA-HA, observed: 84.967, delta from target: 24.033
   A  51  ILE  HA , Angle C-CA-HA, observed: 84.927, delta from target: 24.073
   A 126  VAL  HB , Angle CA-CB-HB, observed: 77.025, delta from target: 31.975
   A 125  LYS  HA , Angle C-CA-HA, observed: 74.415, delta from target: 34.585

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.198   2242  Z= 0.675
    Angle     :  2.971  34.585   4079  Z= 1.302
    Chirality :  1.141   5.042    176
    Planarity :  0.013   0.077    327
    Dihedral  : 16.215 122.809    769
    Min Nonbonded Distance : 1.412
  
  Molprobity Statistics.
    All-atom Clashscore : 18.49
    Ramachandran Plot:
      Outliers : 13.14 %
      Allowed  :  9.49 %
      Favored  : 77.37 %
    Rotamer:
      Outliers :  6.45 %
      Allowed  :  6.45 %
      Favored  : 87.10 %
    Cbeta Deviations : 15.15 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 1.53 %
      Twisted Proline : 0.00 %
      Twisted General : 15.27 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.66 (0.64), residues: 137
    helix: -2.11 (0.49), residues: 69
    sheet:  None (None), residues: 0
    loop : -2.78 (0.76), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A  43 
   PHE   0.124   0.031   PHE A  67 
   TYR   0.141   0.026   TYR A  89 
   ARG   0.028   0.006   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A  43 
   PHE   0.068   0.023   PHE A  15 
   TYR   0.102   0.029   TYR A 111 
   ARG   0.004   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =  13.14 %
                favored =  77.37 %
  Rotamer outliers      =   6.45 %
  C-beta deviations     =    20
  Clashscore            =  18.49
  RMS(bonds)            =   0.0129
  RMS(angles)           =   2.97
  MolProbity score      =   3.15

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.963)
  Mean delta:    0.013 (Z=  0.697)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.11     4.49  1.00e+00  2.01e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.26     4.34  1.00e+00  1.89e+01   4.3*sigma

  Min. delta:    0.006 (Z=  0.004)
  Max. delta:    7.941 (Z=  4.486)
  Mean delta:    1.840 (Z=  1.017)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   153.67    26.33  5.00e+00  2.77e+01   5.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA          0.00   -24.44    24.44  5.00e+00  2.39e+01   4.9*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00  -158.94   -21.06  5.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.081
  Max. delta:   69.678
  Mean delta:   15.162

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.216
  Mean delta:    0.084

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.120       0.207      289.44  10.3*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.077       0.132      119.19   6.6*sigma

  Min. delta:    0.000
  Max. delta:    0.120
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   10" pdbres="HIS A  43  conformer  : HE2, HD1 
   10" pdbres="HIS A 134  conformer  : HE2, HD1 
   10" pdbres="HIS A 135  conformer  : HE2, HD1 
   10" pdbres="HIS A 136  conformer  : HE2, HD1 
   10" pdbres="HIS A 137  conformer  : HE2, HD1 
   10" pdbres="HIS A 138  conformer  : HE2, HD1 
   10" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.041   2242  Z= 0.496
    Angle     :  1.707   7.941   4079  Z= 0.757
    Chirality :  0.084   0.216    176
    Planarity :  0.013   0.115    327
    Dihedral  : 13.669  69.678    769
    Min Nonbonded Distance : 1.693
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.84 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  5.65 %
      Favored  : 88.71 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.89 (0.66), residues: 137
    helix: -0.87 (0.48), residues: 88
    sheet:  None (None), residues: 0
    loop : -1.75 (0.91), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.004   HIS A 139 
   PHE   0.133   0.025   PHE A  45 
   TYR   0.252   0.034   TYR A  50 
   ARG   0.056   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.004   HIS A 139 
   PHE   0.063   0.017   PHE A  45 
   TYR   0.207   0.037   TYR A  50 
   ARG   0.010   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.56    -0.11  1.60e-02  4.38e+01   6.6*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.106 (Z=  6.620)
  Mean delta:    0.014 (Z=  0.748)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   140.50   -18.80  1.80e+00  1.09e+02  10.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   140.02   -18.32  1.80e+00  1.04e+02  10.2*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   126.64   -16.54  1.90e+00  7.58e+01   8.7*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   133.60   -11.90  1.80e+00  4.37e+01   6.6*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00   128.58   -17.58  2.80e+00  3.94e+01   6.3*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    99.98    10.52  1.70e+00  3.83e+01   6.2*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.83   -11.13  1.80e+00  3.82e+01   6.2*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10   121.67   -11.57  1.90e+00  3.71e+01   6.1*sigma
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        121.70   132.60   -10.90  1.80e+00  3.67e+01   6.1*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   120.59   -10.09  1.70e+00  3.52e+01   5.9*sigma
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        121.70   132.38   -10.68  1.80e+00  3.52e+01   5.9*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   120.15    -9.65  1.70e+00  3.22e+01   5.7*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N         116.20   105.57    10.63  2.00e+00  2.83e+01   5.3*sigma
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        121.70   131.09    -9.39  1.80e+00  2.72e+01   5.2*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  CD        112.00   104.85     7.15  1.40e+00  2.61e+01   5.1*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   122.70   -11.40  2.30e+00  2.46e+01   5.0*sigma
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        121.70   130.55    -8.85  1.80e+00  2.41e+01   4.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.49    -4.89  1.00e+00  2.40e+01   4.9*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   119.33    -9.23  1.90e+00  2.36e+01   4.9*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10   100.87     9.23  1.90e+00  2.36e+01   4.9*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   117.38    -4.78  1.00e+00  2.28e+01   4.8*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   124.35   -13.35  2.80e+00  2.27e+01   4.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.03    -9.43  2.00e+00  2.22e+01   4.7*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   115.61     7.39  1.60e+00  2.13e+01   4.6*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   107.60    -4.60  1.10e+00  1.75e+01   4.2*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   129.21    -7.51  1.80e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG1       110.40   117.39    -6.99  1.70e+00  1.69e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   18.801 (Z= 10.445)
  Mean delta:    2.472 (Z=  1.339)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -110.25   -69.75  5.00e+00  1.95e+02  14.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -110.84   -69.16  5.00e+00  1.91e+02  13.8*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   128.01    51.99  5.00e+00  1.08e+02  10.4*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -137.61   -42.39  5.00e+00  7.19e+01   8.5*sigma
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00  -147.87   -32.13  5.00e+00  4.13e+01   6.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA          0.00   -31.92    31.92  5.00e+00  4.08e+01   6.4*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -148.91   -31.09  5.00e+00  3.87e+01   6.2*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -150.85   -29.15  5.00e+00  3.40e+01   5.8*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   153.30    26.70  5.00e+00  2.85e+01   5.3*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00   154.81    25.19  5.00e+00  2.54e+01   5.0*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   155.21    24.79  5.00e+00  2.46e+01   5.0*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   157.08    22.92  5.00e+00  2.10e+01   4.6*sigma

  Min. delta:    0.034
  Max. delta:   69.752
  Mean delta:   14.257

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.50     5.01  2.00e-01  6.27e+02  25.0*sigma
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51    -2.22     4.73  2.00e-01  5.59e+02  23.6*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -1.92     4.43  2.00e-01  4.91e+02  22.2*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.88     4.31  2.00e-01  4.65e+02  21.6*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.83     4.26  2.00e-01  4.53e+02  21.3*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51    -0.59     3.10  2.00e-01  2.40e+02  15.5*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51     1.47     1.04  2.00e-01  2.71e+01   5.2*sigma

  Min. delta:    0.000
  Max. delta:    5.010
  Mean delta:    0.816

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.049       0.094       47.16   4.7*sigma
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CD            0.135       0.234       29.25   4.7*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.091       0.087      164.42   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.135
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    5" pdbres="HIS A  43  conformer  : HE2, HD1 
    5" pdbres="HIS A 134  conformer  : HE2, HD1 
    5" pdbres="HIS A 135  conformer  : HE2, HD1 
    5" pdbres="HIS A 136  conformer  : HE2, HD1 
    5" pdbres="HIS A 137  conformer  : HE2, HD1 
    5" pdbres="HIS A 138  conformer  : HE2, HD1 
    5" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  91  TYR  HA , Angle N-CA-HA, observed: 92.303, delta from target: 17.697
   A  78  ILE  HA , Angle N-CA-HA, observed: 92.163, delta from target: 17.837
   A  91  TYR  HA , Angle CB-CA-HA, observed: 90.360, delta from target: 18.640
   A  79  LYS  HA , Angle CB-CA-HA, observed: 128.952, delta from target: -19.952
   A  89  TYR  HA , Angle C-CA-HA, observed: 88.839, delta from target: 20.161
   A  90  SER  HA , Angle CB-CA-HA, observed: 87.130, delta from target: 21.870

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.010   0.106   2242  Z= 0.532
    Angle     :  2.253  21.870   4079  Z= 0.992
    Chirality :  0.816   5.010    176
    Planarity :  0.014   0.135    327
    Dihedral  : 11.921  69.752    769
    Min Nonbonded Distance : 1.717
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  :  8.03 %
      Favored  : 85.40 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  4.84 %
      Favored  : 91.94 %
    Cbeta Deviations :  6.82 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.76 %
      Twisted Proline : 14.29 %
      Twisted General : 4.58 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.71 (0.67), residues: 137
    helix: -1.13 (0.49), residues: 86
    sheet:  None (None), residues: 0
    loop : -2.89 (0.92), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A  43 
   PHE   0.068   0.012   PHE A  67 
   TYR   0.207   0.026   TYR A  91 
   ARG   0.025   0.006   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.003   HIS A  43 
   PHE   0.048   0.013   PHE A  67 
   TYR   0.158   0.029   TYR A  91 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  1.566)
  Mean delta:    0.001 (Z=  0.062)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    2.615 (Z=  1.372)
  Mean delta:    0.375 (Z=  0.205)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   88.861
  Mean delta:   23.273

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.095
  Mean delta:    0.035

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.001
  Mean delta:    0.000

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    9" pdbres="HIS A  43  conformer  : HE2, HD1 
    9" pdbres="HIS A 134  conformer  : HE2, HD1 
    9" pdbres="HIS A 135  conformer  : HE2, HD1 
    9" pdbres="HIS A 136  conformer  : HE2, HD1 
    9" pdbres="HIS A 137  conformer  : HE2, HD1 
    9" pdbres="HIS A 138  conformer  : HE2, HD1 
    9" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2241  Z= 0.045
    Angle     :  0.980   4.851   4077  Z= 0.342
    Chirality :  0.035   0.095    176
    Planarity :  0.000   0.001    326
    Dihedral  : 18.301  88.861    768
    Min Nonbonded Distance : 1.607
  
  Molprobity Statistics.
    All-atom Clashscore : 19.40
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  : 18.25 %
      Favored  : 77.37 %
    Rotamer:
      Outliers : 21.77 %
      Allowed  : 15.32 %
      Favored  : 62.90 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -6.47 (0.49), residues: 137
    helix: -3.62 (0.41), residues: 67
    sheet:  None (None), residues: 0
    loop : -5.20 (0.55), residues: 70
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.003   0.001   TYR A 111 
   ARG   0.001   0.000   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.001   0.000   PHE A  67 
   TYR   0.001   0.000   TYR A 111 
   ARG   0.000   0.000   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  94.16 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     0
  Clashscore            =   2.71
  RMS(bonds)            =   0.0095
  RMS(angles)           =   1.71
  MolProbity score      =   2.02

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   6.57 %
                favored =  85.40 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     9
  Clashscore            =   8.12
  RMS(bonds)            =   0.0101
  RMS(angles)           =   2.25
  MolProbity score      =   2.48

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   4.38 %
                favored =  77.37 %
  Rotamer outliers      =  21.77 %
  C-beta deviations     =     0
  Clashscore            =  19.40
  RMS(bonds)            =   0.0009
  RMS(angles)           =   0.98
  MolProbity score      =   3.57

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.34     0.12  1.90e-02  3.86e+01   6.2*sigma
   A 126  VAL  CA
   A 126  VAL  C           1.52     1.44     0.08  2.10e-02  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.118 (Z=  6.212)
  Mean delta:    0.015 (Z=  0.773)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20    96.03    20.17  2.00e+00  1.02e+02  10.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.34   -11.44  1.50e+00  5.81e+01   7.6*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   124.57   -14.47  1.90e+00  5.80e+01   7.6*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   135.27   -13.57  1.80e+00  5.69e+01   7.5*sigma
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        121.70   134.89   -13.19  1.80e+00  5.37e+01   7.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   131.65   -10.85  1.70e+00  4.07e+01   6.4*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.51    -5.91  1.00e+00  3.50e+01   5.9*sigma
   A 126  VAL  O
   A 126  VAL  C
   A 127  ARG  N         123.00   132.24    -9.24  1.60e+00  3.33e+01   5.8*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.97   -11.37  2.00e+00  3.23e+01   5.7*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00   126.67   -15.67  2.80e+00  3.13e+01   5.6*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG1       110.40   119.53    -9.13  1.70e+00  2.89e+01   5.4*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   131.27    -9.57  1.80e+00  2.83e+01   5.3*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   112.79     8.91  1.80e+00  2.45e+01   5.0*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   117.51    -4.91  1.00e+00  2.41e+01   4.9*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   129.87    -8.17  1.80e+00  2.06e+01   4.5*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   129.63    -7.93  1.80e+00  1.94e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.52     5.68  1.30e+00  1.91e+01   4.4*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG1       110.40   117.80    -7.40  1.70e+00  1.89e+01   4.4*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.34     4.26  1.00e+00  1.82e+01   4.3*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.69     5.51  1.30e+00  1.80e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.67     7.13  1.70e+00  1.76e+01   4.2*sigma
   A  21  ARG  CD
   A  21  ARG  NE
   A  21  ARG  CZ        124.40   130.25    -5.85  1.40e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.71e+01   4.1*sigma
   A  39  LEU  N
   A  39  LEU  CA
   A  39  LEU  CB        110.50   103.53     6.97  1.70e+00  1.68e+01   4.1*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N         116.20   108.01     8.19  2.00e+00  1.68e+01   4.1*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   128.99    -7.29  1.80e+00  1.64e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   20.172 (Z= 10.086)
  Mean delta:    2.460 (Z=  1.349)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    81.77    98.23  5.00e+00  3.86e+02  19.6*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    96.90    83.10  5.00e+00  2.76e+02  16.6*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   101.98    78.02  5.00e+00  2.43e+02  15.6*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   132.59    47.41  5.00e+00  8.99e+01   9.5*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -134.49   -45.51  5.00e+00  8.29e+01   9.1*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   135.44    44.56  5.00e+00  7.94e+01   8.9*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   139.25    40.75  5.00e+00  6.64e+01   8.2*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00  -139.28   -40.72  5.00e+00  6.63e+01   8.1*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   144.72    35.28  5.00e+00  4.98e+01   7.1*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   145.27    34.73  5.00e+00  4.82e+01   6.9*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   146.79    33.21  5.00e+00  4.41e+01   6.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00  -149.75   -30.25  5.00e+00  3.66e+01   6.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   153.93    26.07  5.00e+00  2.72e+01   5.2*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   156.04    23.96  5.00e+00  2.30e+01   4.8*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   156.50    23.50  5.00e+00  2.21e+01   4.7*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   157.54    22.46  5.00e+00  2.02e+01   4.5*sigma

  Min. delta:    0.056
  Max. delta:   98.232
  Mean delta:   16.980

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.64     5.29  2.00e-01  6.99e+02  26.4*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.38     4.89  2.00e-01  5.98e+02  24.4*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.31     4.75  2.00e-01  5.65e+02  23.8*sigma
   A  77  ILE  CA
   A  77  ILE  N
   A  77  ILE  C
   A  77  ILE  CB          2.43    -2.14     4.57  2.00e-01  5.22e+02  22.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.12     4.55  2.00e-01  5.17e+02  22.7*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.33     3.76  2.00e-01  3.54e+02  18.8*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -0.86     3.29  2.00e-01  2.70e+02  16.4*sigma

  Min. delta:    0.000
  Max. delta:    5.289
  Mean delta:    0.908

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O
   A 125  LYS  N             0.047       0.081       21.82   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.075
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A 126  VAL  HB , Angle CA-CB-HB, observed: 96.279, delta from target: 12.721
   A  71  ILE  HA , Angle N-CA-HA, observed: 96.896, delta from target: 13.104
   A  51  ILE  HA , Angle C-CA-HA, observed: 94.598, delta from target: 14.402
   A 127  ARG  HA , Angle CB-CA-HA, observed: 93.120, delta from target: 15.880
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.540, delta from target: 16.460
   A 122  ILE  HA , Angle N-CA-HA, observed: 89.970, delta from target: 20.030
   A 122  ILE  HA , Angle C-CA-HA, observed: 81.220, delta from target: 27.780

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.118   2242  Z= 0.550
    Angle     :  2.233  27.780   4079  Z= 0.993
    Chirality :  0.908   5.289    176
    Planarity :  0.011   0.075    327
    Dihedral  : 13.810  98.232    769
    Min Nonbonded Distance : 1.735
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  7.30 %
      Allowed  :  9.49 %
      Favored  : 83.21 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  8.06 %
      Favored  : 87.90 %
    Cbeta Deviations :  6.82 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 9.16 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.47 (0.64), residues: 137
    helix: -1.35 (0.57), residues: 62
    sheet:  None (None), residues: 0
    loop : -1.90 (0.69), residues: 75
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A 137 
   PHE   0.081   0.020   PHE A  15 
   TYR   0.089   0.016   TYR A  89 
   ARG   0.044   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A 137 
   PHE   0.049   0.021   PHE A  15 
   TYR   0.074   0.019   TYR A  89 
   ARG   0.007   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   7.30 %
                favored =  83.21 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     9
  Clashscore            =   4.51
  RMS(bonds)            =   0.0106
  RMS(angles)           =   2.23
  MolProbity score      =   2.38

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.874)
  Mean delta:    0.013 (Z=  0.686)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   120.85   -10.35  1.70e+00  3.71e+01   6.1*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   132.56   -10.86  1.80e+00  3.64e+01   6.0*sigma
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   106.63     5.97  1.00e+00  3.56e+01   6.0*sigma
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        121.70   132.21   -10.51  1.80e+00  3.41e+01   5.8*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O         120.80   111.32     9.48  1.70e+00  3.11e+01   5.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20   126.95   -10.75  2.00e+00  2.89e+01   5.4*sigma
   A  99  LEU  C
   A  99  LEU  CA
   A  99  LEU  CB        110.10   118.76    -8.66  1.90e+00  2.08e+01   4.6*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.52     5.68  1.30e+00  1.91e+01   4.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.34     4.26  1.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   10.863 (Z=  6.089)
  Mean delta:    2.088 (Z=  1.143)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00    89.41    90.59  5.00e+00  3.28e+02  18.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -138.06   -41.94  5.00e+00  7.04e+01   8.4*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -139.97   -40.03  5.00e+00  6.41e+01   8.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   147.24    32.76  5.00e+00  4.29e+01   6.6*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00  -153.43   -26.57  5.00e+00  2.82e+01   5.3*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   155.53    24.47  5.00e+00  2.39e+01   4.9*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   155.81    24.19  5.00e+00  2.34e+01   4.8*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00  -156.94   -23.06  5.00e+00  2.13e+01   4.6*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -158.15   -21.85  5.00e+00  1.91e+01   4.4*sigma

  Min. delta:    0.050
  Max. delta:   90.591
  Mean delta:   17.517

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  99  LEU  CA
   A  99  LEU  N
   A  99  LEU  C
   A  99  LEU  CB          2.51    -1.22     3.73  2.00e-01  3.47e+02  18.6*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -1.14     3.65  2.00e-01  3.33e+02  18.2*sigma

  Min. delta:    0.000
  Max. delta:    3.728
  Mean delta:    0.408

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.067       0.118       89.12   5.9*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.049       0.093       48.91   4.7*sigma
   A 123  GLU  CG
   A 123  GLU  CD
   A 123  GLU  OE1
   A 123  GLU  OE2           0.051       0.088       25.66   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.068
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

   12" pdbres="HIS A  43  conformer  : HE2, HD1 
   12" pdbres="HIS A 134  conformer  : HE2, HD1 
   12" pdbres="HIS A 135  conformer  : HE2, HD1 
   12" pdbres="HIS A 136  conformer  : HE2, HD1 
   12" pdbres="HIS A 137  conformer  : HE2, HD1 
   12" pdbres="HIS A 138  conformer  : HE2, HD1 
   12" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  79  LYS  HA , Angle CB-CA-HA, observed: 94.379, delta from target: 14.621
   A  79  LYS  HA , Angle N-CA-HA, observed: 94.845, delta from target: 15.155
   A  99  LEU  HA , Angle C-CA-HA, observed: 90.965, delta from target: 18.035

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.489
    Angle     :  1.904  18.035   4079  Z= 0.844
    Chirality :  0.408   3.728    176
    Planarity :  0.013   0.063    327
    Dihedral  : 14.752  90.591    769
    Min Nonbonded Distance : 1.784
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  6.57 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  1.61 %
      Favored  : 93.55 %
    Cbeta Deviations :  3.03 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.37 (0.68), residues: 137
    helix: -0.08 (0.60), residues: 61
    sheet:  None (None), residues: 0
    loop : -1.64 (0.72), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.026   0.010   HIS A 136 
   PHE   0.049   0.013   PHE A  15 
   TYR   0.143   0.022   TYR A  50 
   ARG   0.055   0.015   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.026   0.010   HIS A 136 
   PHE   0.032   0.012   PHE A  15 
   TYR   0.118   0.024   TYR A  50 
   ARG   0.010   0.003   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  92  THR  N
   A  92  THR  CA          1.46     1.55    -0.10  1.90e-02  2.52e+01   5.0*sigma
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.55    -0.09  1.90e-02  2.43e+01   4.9*sigma
   A  92  THR  CB
   A  92  THR  OG1         1.43     1.36     0.08  1.60e-02  2.29e+01   4.8*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.39    -0.07  1.40e-02  2.16e+01   4.7*sigma
   A  78  ILE  CA
   A  78  ILE  C           1.52     1.61    -0.09  2.10e-02  1.64e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.095 (Z=  5.021)
  Mean delta:    0.016 (Z=  0.815)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   136.56   -14.86  1.80e+00  6.81e+01   8.3*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.18   -11.28  1.50e+00  5.65e+01   7.5*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.14   -12.44  1.80e+00  4.77e+01   6.9*sigma
   A  82  THR  CA
   A  82  THR  CB
   A  82  THR  OG1       109.60   119.95   -10.35  1.50e+00  4.76e+01   6.9*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   132.53   -10.83  1.80e+00  3.62e+01   6.0*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    94.82    16.18  2.80e+00  3.34e+01   5.8*sigma
   A  81  TYR  C
   A  81  TYR  CA
   A  81  TYR  CB        110.10    99.80    10.30  1.90e+00  2.94e+01   5.4*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50   101.29     9.21  1.70e+00  2.93e+01   5.4*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   123.38    -9.48  1.80e+00  2.77e+01   5.3*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   119.28    -8.88  1.70e+00  2.73e+01   5.2*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   119.69    -9.59  1.90e+00  2.55e+01   5.0*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   101.95     8.55  1.70e+00  2.53e+01   5.0*sigma
   A  70  LEU  N
   A  70  LEU  CA
   A  70  LEU  CB        110.50   102.25     8.25  1.70e+00  2.35e+01   4.9*sigma
   A  80  GLY  N
   A  80  GLY  CA
   A  80  GLY  C         113.30    99.38    13.92  2.90e+00  2.30e+01   4.8*sigma
   A 117  PRO  N
   A 117  PRO  CA
   A 117  PRO  C         112.10   123.89   -11.79  2.50e+00  2.22e+01   4.7*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N         116.20   125.42    -9.22  2.00e+00  2.12e+01   4.6*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   120.78    -9.18  2.00e+00  2.11e+01   4.6*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50   103.86     7.64  1.70e+00  2.02e+01   4.5*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   117.09    -4.49  1.00e+00  2.02e+01   4.5*sigma
   A  82  THR  C
   A  82  THR  CA
   A  82  THR  CB        109.10    99.25     9.85  2.20e+00  2.00e+01   4.5*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   129.41    -7.71  1.80e+00  1.83e+01   4.3*sigma
   A  82  THR  N
   A  82  THR  CA
   A  82  THR  C         111.00    99.22    11.78  2.80e+00  1.77e+01   4.2*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.95     6.85  1.70e+00  1.62e+01   4.0*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   122.13    -8.03  2.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:   16.176 (Z=  8.253)
  Mean delta:    2.541 (Z=  1.359)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   -87.61   -92.39  5.00e+00  3.41e+02  18.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -99.28   -80.72  5.00e+00  2.61e+02  16.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   106.24    73.76  5.00e+00  2.18e+02  14.8*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   106.45    73.55  5.00e+00  2.16e+02  14.7*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -122.73   -57.27  5.00e+00  1.31e+02  11.5*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   128.29    51.71  5.00e+00  1.07e+02  10.3*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   133.53    46.47  5.00e+00  8.64e+01   9.3*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   134.45    45.55  5.00e+00  8.30e+01   9.1*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   143.69    36.31  5.00e+00  5.27e+01   7.3*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00  -143.86   -36.14  5.00e+00  5.22e+01   7.2*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   148.26    31.74  5.00e+00  4.03e+01   6.3*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   152.74    27.26  5.00e+00  2.97e+01   5.5*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00  -153.15   -26.85  5.00e+00  2.88e+01   5.4*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -155.43   -24.57  5.00e+00  2.42e+01   4.9*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   156.06    23.94  5.00e+00  2.29e+01   4.8*sigma
   A  43  HIS  CA
   A  43  HIS  C
   A  44  ASP  N
   A  44  ASP  CA        180.00  -158.56   -21.44  5.00e+00  1.84e+01   4.3*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00  -158.74   -21.26  5.00e+00  1.81e+01   4.3*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   158.90    21.10  5.00e+00  1.78e+01   4.2*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   158.90    21.10  5.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.041
  Max. delta:   92.394
  Mean delta:   17.650

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.35     5.86  2.00e-01  8.59e+02  29.3*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -3.21     5.73  2.00e-01  8.22e+02  28.7*sigma
   A  93  LEU  CA
   A  93  LEU  N
   A  93  LEU  C
   A  93  LEU  CB          2.51    -2.73     5.24  2.00e-01  6.86e+02  26.2*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.41     4.92  2.00e-01  6.06e+02  24.6*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51    -2.37     4.88  2.00e-01  5.94e+02  24.4*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -2.18     4.69  2.00e-01  5.50e+02  23.4*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.00     4.51  2.00e-01  5.08e+02  22.5*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.10     3.54  2.00e-01  3.13e+02  17.7*sigma

  Min. delta:    0.000
  Max. delta:    5.862
  Mean delta:    1.069

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.056       0.107       61.88   5.4*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.053       0.105       57.10   5.2*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.055       0.098       61.38   4.9*sigma
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.049       0.087       48.64   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.065
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    2" pdbres="HIS A  43  conformer  : HE2, HD1 
    2" pdbres="HIS A 134  conformer  : HE2, HD1 
    2" pdbres="HIS A 135  conformer  : HE2, HD1 
    2" pdbres="HIS A 136  conformer  : HE2, HD1 
    2" pdbres="HIS A 137  conformer  : HE2, HD1 
    2" pdbres="HIS A 138  conformer  : HE2, HD1 
    2" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  81  TYR  HA , Angle CB-CA-HA, observed: 121.354, delta from target: -12.354
   A  51  ILE  HA , Angle CB-CA-HA, observed: 95.264, delta from target: 13.736
   A  79  LYS  HA , Angle N-CA-HA, observed: 124.626, delta from target: -14.626
   A  74  ASP  HA , Angle C-CA-HA, observed: 93.968, delta from target: 15.032
   A  82  THR  HA , Angle C-CA-HA, observed: 124.378, delta from target: -15.378
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.234, delta from target: 15.766

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.095   2242  Z= 0.580
    Angle     :  2.264  16.176   4079  Z= 0.998
    Chirality :  1.069   5.862    176
    Planarity :  0.012   0.065    327
    Dihedral  : 14.545  92.394    769
    Min Nonbonded Distance : 1.726
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  8.03 %
      Favored  : 87.59 %
    Rotamer:
      Outliers :  8.06 %
      Allowed  :  3.23 %
      Favored  : 88.71 %
    Cbeta Deviations : 11.36 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 8.40 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.88 (0.68), residues: 137
    helix: -1.93 (0.56), residues: 70
    sheet:  None (None), residues: 0
    loop : -1.81 (0.78), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.006   HIS A 134 
   PHE   0.049   0.016   PHE A  15 
   TYR   0.133   0.029   TYR A  89 
   ARG   0.059   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.006   HIS A 134 
   PHE   0.034   0.013   PHE A  15 
   TYR   0.107   0.033   TYR A 111 
   ARG   0.001   0.000   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  91.24 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     4
  Clashscore            =   2.71
  RMS(bonds)            =   0.0095
  RMS(angles)           =   1.90
  MolProbity score      =   2.09

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   4.38 %
                favored =  87.59 %
  Rotamer outliers      =   8.06 %
  C-beta deviations     =    15
  Clashscore            =   6.31
  RMS(bonds)            =   0.0111
  RMS(angles)           =   2.26
  MolProbity score      =   2.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.093 (Z=  3.903)
  Mean delta:    0.015 (Z=  0.785)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    92.98    17.12  1.90e+00  8.12e+01   9.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   129.07   -12.17  1.50e+00  6.59e+01   8.1*sigma
   A  70  LEU  N
   A  70  LEU  CA
   A  70  LEU  CB        110.50    97.00    13.50  1.70e+00  6.31e+01   7.9*sigma
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        121.70   135.76   -14.06  1.80e+00  6.10e+01   7.8*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    97.42    13.08  1.70e+00  5.92e+01   7.7*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   134.64   -12.94  1.80e+00  5.17e+01   7.2*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   126.82   -15.52  2.30e+00  4.55e+01   6.7*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   124.50   -10.60  1.80e+00  3.47e+01   5.9*sigma
   A  76  SER  C
   A  76  SER  CA
   A  76  SER  CB        110.10   120.79   -10.69  1.90e+00  3.16e+01   5.6*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.82   -10.12  1.80e+00  3.16e+01   5.6*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.61   -11.01  2.00e+00  3.03e+01   5.5*sigma
   A 135  HIS  CA
   A 135  HIS  CB
   A 135  HIS  CG        113.80   119.17    -5.37  1.00e+00  2.88e+01   5.4*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10   120.20   -10.10  1.90e+00  2.83e+01   5.3*sigma
   A  82  THR  N
   A  82  THR  CA
   A  82  THR  CB        111.50   120.53    -9.03  1.70e+00  2.82e+01   5.3*sigma
   A  69  ALA  C
   A  70  LEU  N
   A  70  LEU  CA        121.70   131.23    -9.53  1.80e+00  2.80e+01   5.3*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  C         111.00   125.11   -14.11  2.80e+00  2.54e+01   5.0*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   119.62    -9.52  1.90e+00  2.51e+01   5.0*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.43    -4.83  1.00e+00  2.33e+01   4.8*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   130.10    -8.40  1.80e+00  2.18e+01   4.7*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   130.02    -8.32  1.80e+00  2.14e+01   4.6*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   129.93    -8.23  1.80e+00  2.09e+01   4.6*sigma
   A  93  LEU  CD1
   A  93  LEU  CG
   A  93  LEU  CD2       110.80   100.77    10.03  2.20e+00  2.08e+01   4.6*sigma
   A  78  ILE  N
   A  78  ILE  CA
   A  78  ILE  C         111.00   123.38   -12.38  2.80e+00  1.95e+01   4.4*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   120.42    -8.82  2.00e+00  1.95e+01   4.4*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   107.39     8.81  2.00e+00  1.94e+01   4.4*sigma
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        121.70   129.60    -7.90  1.80e+00  1.92e+01   4.4*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  51  ILE  O         120.80   113.37     7.43  1.70e+00  1.91e+01   4.4*sigma
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        121.70   129.55    -7.85  1.80e+00  1.90e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.60     5.60  1.30e+00  1.85e+01   4.3*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   129.44    -7.74  1.80e+00  1.85e+01   4.3*sigma
   A  90  SER  C
   A  90  SER  CA
   A  90  SER  CB        110.10   118.21    -8.11  1.90e+00  1.82e+01   4.3*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG2       110.50   117.72    -7.22  1.70e+00  1.81e+01   4.2*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   116.83    -4.23  1.00e+00  1.79e+01   4.2*sigma
   A  39  LEU  N
   A  39  LEU  CA
   A  39  LEU  CB        110.50   103.41     7.09  1.70e+00  1.74e+01   4.2*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   129.10    -7.40  1.80e+00  1.69e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:   17.119 (Z=  9.010)
  Mean delta:    2.718 (Z=  1.453)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   -89.07   -90.93  5.00e+00  3.31e+02  18.2*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -110.33   -69.67  5.00e+00  1.94e+02  13.9*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   129.82    50.18  5.00e+00  1.01e+02  10.0*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   131.93    48.07  5.00e+00  9.24e+01   9.6*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   134.74    45.26  5.00e+00  8.19e+01   9.1*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   140.78    39.22  5.00e+00  6.15e+01   7.8*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -141.77   -38.23  5.00e+00  5.85e+01   7.6*sigma
   A  99  LEU  CA
   A  99  LEU  C
   A 100  GLN  N
   A 100  GLN  CA        180.00   144.38    35.62  5.00e+00  5.08e+01   7.1*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -144.58   -35.42  5.00e+00  5.02e+01   7.1*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   147.83    32.17  5.00e+00  4.14e+01   6.4*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   150.70    29.30  5.00e+00  3.43e+01   5.9*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -154.39   -25.61  5.00e+00  2.62e+01   5.1*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -157.13   -22.87  5.00e+00  2.09e+01   4.6*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   158.02    21.98  5.00e+00  1.93e+01   4.4*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   158.04    21.96  5.00e+00  1.93e+01   4.4*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   158.05    21.95  5.00e+00  1.93e+01   4.4*sigma

  Min. delta:    0.021
  Max. delta:   90.934
  Mean delta:   16.776

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.03     5.54  2.00e-01  7.67e+02  27.7*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -2.59     5.23  2.00e-01  6.85e+02  26.2*sigma
   A  82  THR  CB
   A  82  THR  CA
   A  82  THR  OG1
   A  82  THR  CG2         2.55    -2.52     5.08  2.00e-01  6.44e+02  25.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -2.42     4.97  2.00e-01  6.17e+02  24.8*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.30     4.82  2.00e-01  5.81e+02  24.1*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.25     4.76  2.00e-01  5.66e+02  23.8*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -1.76     4.28  2.00e-01  4.57e+02  21.4*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.96     3.39  2.00e-01  2.88e+02  17.0*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -0.59     3.03  2.00e-01  2.29e+02  15.1*sigma
   A  82  THR  CA
   A  82  THR  N
   A  82  THR  C
   A  82  THR  CB          2.53     0.21     2.31  2.00e-01  1.34e+02  11.6*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     1.65     0.86  2.00e-01  1.84e+01   4.3*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51     1.71     0.80  2.00e-01  1.60e+01   4.0*sigma

  Min. delta:    0.001
  Max. delta:    5.540
  Mean delta:    1.076

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.080       0.145      127.11   7.2*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.100       0.125      200.35   6.2*sigma
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.074       0.087       95.29   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.100
  Mean delta:    0.018

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  78  ILE  HA , Angle N-CA-HA, observed: 97.783, delta from target: 12.217
   A  76  SER  HA , Angle C-CA-HA, observed: 93.633, delta from target: 15.367
   A  91  TYR  HA , Angle C-CA-HA, observed: 93.621, delta from target: 15.379
   A  81  TYR  HA , Angle C-CA-HA, observed: 92.392, delta from target: 16.608
   A  51  ILE  HA , Angle CB-CA-HA, observed: 92.062, delta from target: 16.938
   A  51  ILE  HA , Angle C-CA-HA, observed: 89.921, delta from target: 19.079
   A  74  ASP  HA , Angle C-CA-HA, observed: 87.995, delta from target: 21.005
   A  79  LYS  HA , Angle CB-CA-HA, observed: 130.724, delta from target: -21.724
   A  78  ILE  HA , Angle C-CA-HA, observed: 74.531, delta from target: 34.469
   A  82  THR  HA , Angle N-CA-HA, observed: 66.250, delta from target: 43.750

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.011   0.093   2242  Z= 0.559
    Angle     :  2.538  43.750   4079  Z= 1.097
    Chirality :  1.076   5.540    176
    Planarity :  0.014   0.107    327
    Dihedral  : 14.275  90.934    769
    Min Nonbonded Distance : 1.666
  
  Molprobity Statistics.
    All-atom Clashscore : 15.78
    Ramachandran Plot:
      Outliers :  7.30 %
      Allowed  :  8.76 %
      Favored  : 83.94 %
    Rotamer:
      Outliers :  8.87 %
      Allowed  :  4.03 %
      Favored  : 87.10 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 7.63 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.26 (0.67), residues: 137
    helix: -2.09 (0.49), residues: 73
    sheet:  None (None), residues: 0
    loop : -2.16 (0.84), residues: 64
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.005   HIS A 135 
   PHE   0.184   0.026   PHE A  15 
   TYR   0.256   0.027   TYR A  81 
   ARG   0.048   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.005   HIS A 135 
   PHE   0.116   0.025   PHE A  15 
   TYR   0.190   0.031   TYR A  81 
   ARG   0.002   0.000   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 135  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  92  THR  N
   A  92  THR  CA          1.46     1.34     0.12  1.90e-02  4.06e+01   6.4*sigma
   A  91  TYR  CA
   A  91  TYR  C           1.52     1.40     0.12  2.10e-02  3.41e+01   5.8*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.52    -0.07  1.60e-02  1.80e+01   4.2*sigma
   A  91  TYR  C
   A  92  THR  N           1.33     1.27     0.06  1.40e-02  1.79e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.123 (Z=  6.370)
  Mean delta:    0.017 (Z=  0.887)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   133.16   -22.66  1.70e+00  1.78e+02  13.3*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30    88.29    21.01  2.00e+00  1.10e+02  10.5*sigma
   A 126  VAL  CA
   A 126  VAL  CB
   A 126  VAL  CG2       110.40   125.57   -15.17  1.70e+00  7.96e+01   8.9*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   127.21   -15.81  1.90e+00  6.93e+01   8.3*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   124.54   -14.04  1.70e+00  6.82e+01   8.3*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   110.08    12.92  1.60e+00  6.52e+01   8.1*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   107.29    14.41  1.80e+00  6.41e+01   8.0*sigma
   A  91  TYR  C
   A  91  TYR  CA
   A  91  TYR  CB        110.10    95.06    15.04  1.90e+00  6.27e+01   7.9*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  C         111.00    88.96    22.04  2.80e+00  6.20e+01   7.9*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   126.64   -15.04  2.00e+00  5.66e+01   7.5*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   131.19   -14.99  2.00e+00  5.61e+01   7.5*sigma
   A  93  LEU  N
   A  93  LEU  CA
   A  93  LEU  CB        110.50   122.60   -12.10  1.70e+00  5.07e+01   7.1*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   102.38    13.82  2.00e+00  4.77e+01   6.9*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   122.26   -12.16  1.90e+00  4.10e+01   6.4*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   133.02   -11.32  1.80e+00  3.96e+01   6.3*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   122.60   -13.50  2.20e+00  3.77e+01   6.1*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   124.77   -10.87  1.80e+00  3.65e+01   6.0*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   110.96    10.74  1.80e+00  3.56e+01   6.0*sigma
   A  98  SER  N
   A  98  SER  CA
   A  98  SER  C         111.00   126.86   -15.86  2.80e+00  3.21e+01   5.7*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD1       110.70   127.39   -16.69  3.00e+00  3.09e+01   5.6*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.68    -9.98  1.80e+00  3.07e+01   5.5*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   119.70    -9.20  1.70e+00  2.93e+01   5.4*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   100.00    10.10  1.90e+00  2.83e+01   5.3*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N         116.20   105.62    10.58  2.00e+00  2.80e+01   5.3*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   122.17   -10.57  2.00e+00  2.79e+01   5.3*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   131.10    -9.40  1.80e+00  2.73e+01   5.2*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N         116.20   106.22     9.98  2.00e+00  2.49e+01   5.0*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   106.34     9.86  2.00e+00  2.43e+01   4.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   117.50    -4.90  1.00e+00  2.40e+01   4.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   128.92    -8.12  1.70e+00  2.28e+01   4.8*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20   106.65     9.55  2.00e+00  2.28e+01   4.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O         120.80   128.90    -8.10  1.70e+00  2.27e+01   4.8*sigma
   A  92  THR  N
   A  92  THR  CA
   A  92  THR  CB        111.50   103.61     7.89  1.70e+00  2.16e+01   4.6*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   123.86   -12.86  2.80e+00  2.11e+01   4.6*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   107.35     8.85  2.00e+00  1.96e+01   4.4*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG2       110.50   117.85    -7.35  1.70e+00  1.87e+01   4.3*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.67     5.53  1.30e+00  1.81e+01   4.3*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   122.90   -11.90  2.80e+00  1.80e+01   4.2*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   129.34    -7.64  1.80e+00  1.80e+01   4.2*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   114.08     7.62  1.80e+00  1.79e+01   4.2*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.73     5.47  1.30e+00  1.77e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.75e+01   4.2*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   122.46    -8.36  2.00e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.75e+01   4.2*sigma
   A 122  ILE  C
   A 122  ILE  CA
   A 122  ILE  CB        111.60   119.91    -8.31  2.00e+00  1.73e+01   4.2*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.82     5.38  1.30e+00  1.71e+01   4.1*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   116.71    -4.11  1.00e+00  1.69e+01   4.1*sigma
   A 132  LEU  N
   A 132  LEU  CA
   A 132  LEU  C         111.00   122.49   -11.49  2.80e+00  1.68e+01   4.1*sigma
   A  52  PRO  C
   A  52  PRO  CA
   A  52  PRO  CB        110.10   117.89    -7.79  1.90e+00  1.68e+01   4.1*sigma
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        121.70   114.32     7.38  1.80e+00  1.68e+01   4.1*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  C         111.00    99.55    11.45  2.80e+00  1.67e+01   4.1*sigma
   A  93  LEU  CD1
   A  93  LEU  CG
   A  93  LEU  CD2       110.80   101.92     8.88  2.20e+00  1.63e+01   4.0*sigma

  Min. delta:    0.006 (Z=  0.001)
  Max. delta:   22.663 (Z= 13.331)
  Mean delta:    3.035 (Z=  1.598)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -57.58  -122.42  5.00e+00  5.99e+02  24.5*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   -59.51  -120.49  5.00e+00  5.81e+02  24.1*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    68.57   111.43  5.00e+00  4.97e+02  22.3*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00    73.40   106.60  5.00e+00  4.55e+02  21.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   -77.96  -102.04  5.00e+00  4.16e+02  20.4*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00   -84.56   -95.44  5.00e+00  3.64e+02  19.1*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00  -100.78   -79.22  5.00e+00  2.51e+02  15.8*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   103.37    76.63  5.00e+00  2.35e+02  15.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -111.17   -68.83  5.00e+00  1.90e+02  13.8*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00  -116.30   -63.70  5.00e+00  1.62e+02  12.7*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   120.94    59.06  5.00e+00  1.40e+02  11.8*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00  -121.38   -58.62  5.00e+00  1.37e+02  11.7*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   132.75    47.25  5.00e+00  8.93e+01   9.5*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   136.96    43.04  5.00e+00  7.41e+01   8.6*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00   137.27    42.73  5.00e+00  7.30e+01   8.5*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -143.81   -36.19  5.00e+00  5.24e+01   7.2*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   145.76    34.24  5.00e+00  4.69e+01   6.8*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00  -153.46   -26.54  5.00e+00  2.82e+01   5.3*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   154.57    25.43  5.00e+00  2.59e+01   5.1*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   154.78    25.22  5.00e+00  2.55e+01   5.0*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   155.83    24.17  5.00e+00  2.34e+01   4.8*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   156.36    23.64  5.00e+00  2.24e+01   4.7*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   156.86    23.14  5.00e+00  2.14e+01   4.6*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00   157.01    22.99  5.00e+00  2.11e+01   4.6*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   157.46    22.54  5.00e+00  2.03e+01   4.5*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   158.08    21.92  5.00e+00  1.92e+01   4.4*sigma
   A  17  SER  CA
   A  17  SER  C
   A  18  VAL  N
   A  18  VAL  CA        180.00   158.90    21.10  5.00e+00  1.78e+01   4.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -159.84   -20.16  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.027
  Max. delta:  122.416
  Mean delta:   21.480

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 131  ILE  CB
   A 131  ILE  CA
   A 131  ILE  CG1
   A 131  ILE  CG2         2.64    -2.51     5.16  2.00e-01  6.65e+02  25.8*sigma
   A  52  PRO  CA
   A  52  PRO  N
   A  52  PRO  C
   A  52  PRO  CB          2.72    -2.41     5.12  2.00e-01  6.57e+02  25.6*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44    -2.64     5.08  2.00e-01  6.45e+02  25.4*sigma
   A 139  HIS  CA
   A 139  HIS  N
   A 139  HIS  C
   A 139  HIS  CB          2.51    -2.43     4.94  2.00e-01  6.09e+02  24.7*sigma
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -2.38     4.89  2.00e-01  5.97e+02  24.4*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.31     4.82  2.00e-01  5.80e+02  24.1*sigma
   A 122  ILE  CA
   A 122  ILE  N
   A 122  ILE  C
   A 122  ILE  CB          2.43    -2.19     4.63  2.00e-01  5.35e+02  23.1*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -2.09     4.60  2.00e-01  5.28e+02  23.0*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.05     4.57  2.00e-01  5.23e+02  22.9*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51    -1.87     4.38  2.00e-01  4.79e+02  21.9*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.78     4.21  2.00e-01  4.44e+02  21.1*sigma

  Min. delta:    0.001
  Max. delta:    5.158
  Mean delta:    1.203

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.055       0.097       60.68   4.9*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.044       0.082       38.17   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.060
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    3" pdbres="HIS A  43  conformer  : HE2, HD1 
    3" pdbres="HIS A 134  conformer  : HE2, HD1 
    3" pdbres="HIS A 135  conformer  : HE2, HD1 
    3" pdbres="HIS A 136  conformer  : HE2, HD1 
    3" pdbres="HIS A 137  conformer  : HE2, HD1 
    3" pdbres="HIS A 138  conformer  : HE2, HD1 
    3" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  98  SER  HA , Angle N-CA-HA, observed: 97.702, delta from target: 12.298
   A 127  ARG  HA , Angle C-CA-HA, observed: 96.374, delta from target: 12.626
   A 126  VAL  HA , Angle CB-CA-HA, observed: 96.051, delta from target: 12.949
   A  98  SER  HA , Angle C-CA-HA, observed: 96.015, delta from target: 12.985
   A 123  GLU  HA , Angle CB-CA-HA, observed: 95.222, delta from target: 13.778
   A  92  THR  HA , Angle C-CA-HA, observed: 95.139, delta from target: 13.861
   A 126  VAL  HB , Angle CA-CB-HB, observed: 94.644, delta from target: 14.356
   A  93  LEU  HG , Angle CD2-CG-HG, observed: 122.456, delta from target: -14.456
   A 130  SER  HA , Angle N-CA-HA, observed: 95.264, delta from target: 14.736
   A  93  LEU  HA , Angle C-CA-HA, observed: 124.036, delta from target: -15.036
   A  93  LEU  HG , Angle CB-CG-HG, observed: 92.319, delta from target: 16.681
   A  92  THR  HB , Angle CA-CB-HB, observed: 90.569, delta from target: 18.431
   A  91  TYR  HA , Angle C-CA-HA, observed: 129.819, delta from target: -20.819
   A 126  VAL  HA , Angle N-CA-HA, observed: 131.072, delta from target: -21.072
   A  78  ILE  HA , Angle CB-CA-HA, observed: 87.866, delta from target: 21.134
   A  92  THR  HB , Angle OG1-CB-HB, observed: 134.205, delta from target: -25.205

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.012   0.123   2242  Z= 0.632
    Angle     :  2.655  25.205   4079  Z= 1.166
    Chirality :  1.203   5.158    176
    Planarity :  0.011   0.060    327
    Dihedral  : 17.108 122.416    769
    Min Nonbonded Distance : 1.500
  
  Molprobity Statistics.
    All-atom Clashscore : 15.78
    Ramachandran Plot:
      Outliers : 10.22 %
      Allowed  :  8.76 %
      Favored  : 81.02 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  1.61 %
      Favored  : 91.13 %
    Cbeta Deviations : 10.61 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 14.29 %
      Twisted General : 12.21 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.30 (0.67), residues: 137
    helix: -1.47 (0.57), residues: 61
    sheet:  None (None), residues: 0
    loop : -2.93 (0.73), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A 138 
   PHE   0.076   0.021   PHE A  45 
   TYR   0.115   0.017   TYR A  12 
   ARG   0.025   0.005   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A 138 
   PHE   0.052   0.024   PHE A  45 
   TYR   0.097   0.020   TYR A  12 
   ARG   0.002   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   7.30 %
                favored =  83.94 %
  Rotamer outliers      =   8.87 %
  C-beta deviations     =    14
  Clashscore            =  15.78
  RMS(bonds)            =   0.0108
  RMS(angles)           =   2.54
  MolProbity score      =   3.10

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =  10.22 %
                favored =  81.02 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    14
  Clashscore            =  15.78
  RMS(bonds)            =   0.0121
  RMS(angles)           =   2.65
  MolProbity score      =   3.08

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 132  LEU  N
   A 132  LEU  CA          1.46     1.60    -0.14  1.90e-02  5.60e+01   7.5*sigma
   A 127  ARG  CA
   A 127  ARG  C           1.52     1.64    -0.12  2.10e-02  3.02e+01   5.5*sigma
   A 129  ARG  N
   A 129  ARG  CA          1.46     1.56    -0.10  1.90e-02  2.61e+01   5.1*sigma
   A 124  ALA  C
   A 125  LYS  N           1.33     1.26     0.07  1.40e-02  2.37e+01   4.9*sigma
   A 126  VAL  C
   A 127  ARG  N           1.33     1.26     0.06  1.40e-02  2.15e+01   4.6*sigma
   A 127  ARG  CA
   A 127  ARG  CB          1.53     1.62    -0.09  2.00e-02  2.06e+01   4.5*sigma
   A 131  ILE  CA
   A 131  ILE  C           1.52     1.62    -0.09  2.10e-02  1.96e+01   4.4*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.54    -0.08  1.90e-02  1.94e+01   4.4*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     1.54    -0.08  1.90e-02  1.74e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.142 (Z=  7.486)
  Mean delta:    0.018 (Z=  0.948)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   141.13   -31.03  1.90e+00  2.67e+02  16.3*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50    88.49    23.01  1.70e+00  1.83e+02  13.5*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40    88.72    22.68  1.90e+00  1.43e+02  11.9*sigma
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        121.70   100.25    21.45  1.80e+00  1.42e+02  11.9*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   127.09   -16.59  1.70e+00  9.52e+01   9.8*sigma
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   137.48   -15.78  1.80e+00  7.68e+01   8.8*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  CB        111.50    97.08    14.42  1.70e+00  7.20e+01   8.5*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  CB        110.50    96.08    14.42  1.70e+00  7.19e+01   8.5*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    88.46    22.54  2.80e+00  6.48e+01   8.1*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   128.15   -11.25  1.50e+00  5.63e+01   7.5*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   133.86   -12.16  1.80e+00  4.56e+01   6.8*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80    96.12    14.68  2.20e+00  4.46e+01   6.7*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    97.78    12.32  1.90e+00  4.21e+01   6.5*sigma
   A 131  ILE  C
   A 131  ILE  CA
   A 131  ILE  CB        111.60   124.44   -12.84  2.00e+00  4.12e+01   6.4*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   133.19   -11.49  1.80e+00  4.08e+01   6.4*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   133.13   -11.43  1.80e+00  4.03e+01   6.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   131.57   -10.77  1.70e+00  4.01e+01   6.3*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30    96.65    12.65  2.00e+00  4.00e+01   6.3*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   121.15   -10.65  1.70e+00  3.93e+01   6.3*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   119.62    -9.12  1.50e+00  3.70e+01   6.1*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   118.58    -5.98  1.00e+00  3.58e+01   6.0*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   131.94   -10.24  1.80e+00  3.23e+01   5.7*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   127.39   -11.19  2.00e+00  3.13e+01   5.6*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N         116.20   105.21    10.99  2.00e+00  3.02e+01   5.5*sigma
   A 129  ARG  O
   A 129  ARG  C
   A 130  SER  N         123.00   131.68    -8.68  1.60e+00  2.94e+01   5.4*sigma
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        121.70   111.96     9.74  1.80e+00  2.93e+01   5.4*sigma
   A  81  TYR  N
   A  81  TYR  CA
   A  81  TYR  CB        110.50   119.41    -8.91  1.70e+00  2.75e+01   5.2*sigma
   A  51  ILE  C
   A  51  ILE  CA
   A  51  ILE  CB        111.60   121.99   -10.39  2.00e+00  2.70e+01   5.2*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   130.94    -9.24  1.80e+00  2.63e+01   5.1*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  C         111.00   125.34   -14.34  2.80e+00  2.62e+01   5.1*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N         116.20   106.02    10.18  2.00e+00  2.59e+01   5.1*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   130.44    -8.74  1.80e+00  2.36e+01   4.9*sigma
   A 127  ARG  O
   A 127  ARG  C
   A 128  MET  N         123.00   115.39     7.61  1.60e+00  2.26e+01   4.8*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   129.97    -8.27  1.80e+00  2.11e+01   4.6*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.45     5.75  1.30e+00  1.95e+01   4.4*sigma
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        121.70   129.59    -7.89  1.80e+00  1.92e+01   4.4*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG1       110.40   117.85    -7.45  1.70e+00  1.92e+01   4.4*sigma
   A 132  LEU  N
   A 132  LEU  CA
   A 132  LEU  C         111.00   122.99   -11.99  2.80e+00  1.83e+01   4.3*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20   107.77     8.43  2.00e+00  1.78e+01   4.2*sigma
   A  51  ILE  N
   A  51  ILE  CA
   A  51  ILE  CB        111.50   118.64    -7.14  1.70e+00  1.77e+01   4.2*sigma
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        121.70   129.24    -7.54  1.80e+00  1.76e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.45     4.15  1.00e+00  1.73e+01   4.2*sigma
   A  99  LEU  N
   A  99  LEU  CA
   A  99  LEU  CB        110.50   103.59     6.91  1.70e+00  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   31.035 (Z= 16.334)
  Mean delta:    3.211 (Z=  1.699)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00    56.97   123.03  5.00e+00  6.05e+02  24.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    57.13   122.87  5.00e+00  6.04e+02  24.6*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00    81.65    98.35  5.00e+00  3.87e+02  19.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00    87.98    92.02  5.00e+00  3.39e+02  18.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00    88.34    91.66  5.00e+00  3.36e+02  18.3*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00    95.27    84.73  5.00e+00  2.87e+02  16.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00    99.09    80.91  5.00e+00  2.62e+02  16.2*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   100.09    79.91  5.00e+00  2.55e+02  16.0*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   113.93    66.07  5.00e+00  1.75e+02  13.2*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   114.67    65.33  5.00e+00  1.71e+02  13.1*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -117.19   -62.81  5.00e+00  1.58e+02  12.6*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -120.46   -59.54  5.00e+00  1.42e+02  11.9*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00  -120.95   -59.05  5.00e+00  1.39e+02  11.8*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -124.91   -55.09  5.00e+00  1.21e+02  11.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   126.52    53.48  5.00e+00  1.14e+02  10.7*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   130.99    49.01  5.00e+00  9.61e+01   9.8*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -134.74   -45.26  5.00e+00  8.19e+01   9.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00  -135.04   -44.96  5.00e+00  8.09e+01   9.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   135.47    44.53  5.00e+00  7.93e+01   8.9*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -137.07   -42.93  5.00e+00  7.37e+01   8.6*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   147.28    32.72  5.00e+00  4.28e+01   6.5*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA          0.00    30.90   -30.90  5.00e+00  3.82e+01   6.2*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -152.30   -27.70  5.00e+00  3.07e+01   5.5*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   152.98    27.02  5.00e+00  2.92e+01   5.4*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00  -154.89   -25.11  5.00e+00  2.52e+01   5.0*sigma
   A  72  ASN  CA
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        180.00  -155.11   -24.89  5.00e+00  2.48e+01   5.0*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -155.17   -24.83  5.00e+00  2.47e+01   5.0*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00  -155.29   -24.71  5.00e+00  2.44e+01   4.9*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   156.58    23.42  5.00e+00  2.19e+01   4.7*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA          0.00   -20.66    20.66  5.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.017
  Max. delta:  123.031
  Mean delta:   21.818

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -3.32     5.83  2.00e-01  8.49e+02  29.1*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64    -2.68     5.33  2.00e-01  7.10e+02  26.6*sigma
   A  91  TYR  CA
   A  91  TYR  N
   A  91  TYR  C
   A  91  TYR  CB          2.51    -2.51     5.02  2.00e-01  6.29e+02  25.1*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51    -2.44     4.95  2.00e-01  6.13e+02  24.8*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -2.47     4.90  2.00e-01  6.00e+02  24.5*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53    -2.30     4.82  2.00e-01  5.81e+02  24.1*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -2.32     4.81  2.00e-01  5.78e+02  24.0*sigma
   A  98  SER  CA
   A  98  SER  N
   A  98  SER  C
   A  98  SER  CB          2.51    -2.26     4.77  2.00e-01  5.68e+02  23.8*sigma
   A  74  ASP  CA
   A  74  ASP  N
   A  74  ASP  C
   A  74  ASP  CB          2.51    -1.91     4.42  2.00e-01  4.89e+02  22.1*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -0.78     3.21  2.00e-01  2.58e+02  16.1*sigma
   A  81  TYR  CA
   A  81  TYR  N
   A  81  TYR  C
   A  81  TYR  CB          2.51     1.03     1.48  2.00e-01  5.46e+01   7.4*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     1.15     1.36  2.00e-01  4.60e+01   6.8*sigma
   A 126  VAL  CA
   A 126  VAL  N
   A 126  VAL  C
   A 126  VAL  CB          2.44     3.45    -1.00  2.00e-01  2.52e+01   5.0*sigma
   A 129  ARG  CA
   A 129  ARG  N
   A 129  ARG  C
   A 129  ARG  CB          2.51     1.71     0.81  2.00e-01  1.62e+01   4.0*sigma

  Min. delta:    0.001
  Max. delta:    5.826
  Mean delta:    1.180

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.265       0.476     1403.89  23.8*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.053       0.097       56.23   4.9*sigma
   A  83  THR  CA
   A  83  THR  C
   A  83  THR  O
   A  84  GLU  N             0.051       0.088       26.06   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.265
  Mean delta:    0.024

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    3" pdbres="HIS A  43  conformer  : HE2, HD1 
    3" pdbres="HIS A 134  conformer  : HE2, HD1 
    3" pdbres="HIS A 135  conformer  : HE2, HD1 
    3" pdbres="HIS A 136  conformer  : HE2, HD1 
    3" pdbres="HIS A 137  conformer  : HE2, HD1 
    3" pdbres="HIS A 138  conformer  : HE2, HD1 
    3" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  85  LYS  HA , Angle N-CA-HA, observed: 97.321, delta from target: 12.679
   A  92  THR  HB , Angle OG1-CB-HB, observed: 121.936, delta from target: -12.936
   A 128  MET  HA , Angle N-CA-HA, observed: 123.589, delta from target: -13.589
   A 129  ARG  HA , Angle CB-CA-HA, observed: 94.126, delta from target: 14.874
   A  79  LYS  HA , Angle CB-CA-HA, observed: 124.012, delta from target: -15.012
   A  74  ASP  HA , Angle C-CA-HA, observed: 93.110, delta from target: 15.890
   A  51  ILE  HA , Angle C-CA-HA, observed: 92.801, delta from target: 16.199
   A 129  ARG  HA , Angle N-CA-HA, observed: 93.240, delta from target: 16.760
   A  81  TYR  HA , Angle N-CA-HA, observed: 91.905, delta from target: 18.095
   A 131  ILE  HA , Angle C-CA-HA, observed: 89.420, delta from target: 19.580
   A  51  ILE  HA , Angle CB-CA-HA, observed: 88.003, delta from target: 20.997
   A 127  ARG  HA , Angle CB-CA-HA, observed: 84.968, delta from target: 24.032
   A 126  VAL  HA , Angle CB-CA-HA, observed: 134.011, delta from target: -25.011
   A 127  ARG  HA , Angle C-CA-HA, observed: 79.825, delta from target: 29.175
   A 127  ARG  HA , Angle N-CA-HA, observed: 142.384, delta from target: -32.384

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.142   2242  Z= 0.675
    Angle     :  2.860  32.384   4079  Z= 1.252
    Chirality :  1.180   5.826    176
    Planarity :  0.018   0.261    327
    Dihedral  : 17.599 123.031    769
    Min Nonbonded Distance : 1.491
  
  Molprobity Statistics.
    All-atom Clashscore : 18.03
    Ramachandran Plot:
      Outliers : 10.22 %
      Allowed  : 14.60 %
      Favored  : 75.18 %
    Rotamer:
      Outliers :  7.26 %
      Allowed  :  5.65 %
      Favored  : 87.10 %
    Cbeta Deviations : 12.88 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.76 %
      Twisted Proline : 0.00 %
      Twisted General : 16.79 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -4.73 (0.59), residues: 137
    helix: -2.43 (0.47), residues: 70
    sheet:  None (None), residues: 0
    loop : -4.03 (0.69), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 138 
   PHE   0.064   0.014   PHE A  15 
   TYR   0.611   0.036   TYR A  91 
   ARG   0.054   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 138 
   PHE   0.046   0.012   PHE A  15 
   TYR   0.476   0.042   TYR A  91 
   ARG   0.002   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =  10.22 %
                favored =  75.18 %
  Rotamer outliers      =   7.26 %
  C-beta deviations     =    17
  Clashscore            =  18.03
  RMS(bonds)            =   0.0131
  RMS(angles)           =   2.86
  MolProbity score      =   3.20

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A  79  LYS  N
   A  79  LYS  CA          1.46     1.74    -0.29  1.90e-02  2.28e+02  15.1*sigma
   A  93  LEU  CB
   A  93  LEU  CG          1.53     1.79    -0.26  2.00e-02  1.67e+02  12.9*sigma
   A 127  ARG  N
   A 127  ARG  CA          1.46     1.65    -0.20  1.90e-02  1.06e+02  10.3*sigma
   A  93  LEU  CA
   A  93  LEU  CB          1.53     1.33     0.20  2.00e-02  1.04e+02  10.2*sigma
   A 122  ILE  N
   A 122  ILE  CA          1.46     1.65    -0.19  1.90e-02  1.04e+02  10.2*sigma
   A 121  GLY  CA
   A 121  GLY  C           1.52     1.68    -0.17  1.80e-02  8.78e+01   9.4*sigma
   A  80  GLY  N
   A  80  GLY  CA          1.45     1.60    -0.15  1.60e-02  8.59e+01   9.3*sigma
   A  91  TYR  C
   A  92  THR  N           1.33     1.45    -0.12  1.40e-02  6.94e+01   8.3*sigma
   A  78  ILE  C
   A  79  LYS  N           1.33     1.44    -0.11  1.40e-02  6.69e+01   8.2*sigma
   A  93  LEU  CG
   A  93  LEU  CD2         1.52     1.79    -0.26  3.30e-02  6.43e+01   8.0*sigma
   A  88  ASP  CA
   A  88  ASP  C           1.52     1.69    -0.16  2.10e-02  5.83e+01   7.6*sigma
   A 130  SER  N
   A 130  SER  CA          1.46     1.60    -0.14  1.90e-02  5.80e+01   7.6*sigma
   A  94  GLY  C
   A  95  ASP  N           1.33     1.23     0.10  1.40e-02  5.31e+01   7.3*sigma
   A  77  ILE  C
   A  78  ILE  N           1.33     1.23     0.09  1.40e-02  4.55e+01   6.7*sigma
   A  79  LYS  CA
   A  79  LYS  CB          1.53     1.66    -0.13  2.00e-02  4.28e+01   6.5*sigma
   A  92  THR  CB
   A  92  THR  OG1         1.43     1.33     0.10  1.60e-02  4.00e+01   6.3*sigma
   A  93  LEU  N
   A  93  LEU  CA          1.46     1.57    -0.12  1.90e-02  3.77e+01   6.1*sigma
   A  95  ASP  CA
   A  95  ASP  CB          1.53     1.64    -0.11  2.00e-02  3.07e+01   5.5*sigma
   A  77  ILE  CA
   A  77  ILE  CB          1.54     1.69    -0.15  2.70e-02  2.99e+01   5.5*sigma
   A  92  THR  CA
   A  92  THR  C           1.52     1.41     0.11  2.10e-02  2.96e+01   5.4*sigma
   A  92  THR  C
   A  93  LEU  N           1.33     1.25     0.07  1.40e-02  2.80e+01   5.3*sigma
   A 123  GLU  C
   A 124  ALA  N           1.33     1.26     0.07  1.40e-02  2.77e+01   5.3*sigma
   A  92  THR  N
   A  92  THR  CA          1.46     1.55    -0.09  1.90e-02  2.37e+01   4.9*sigma
   A  79  LYS  C
   A  80  GLY  N           1.33     1.26     0.07  1.40e-02  2.28e+01   4.8*sigma
   A  81  TYR  C
   A  82  THR  N           1.33     1.40    -0.07  1.40e-02  2.25e+01   4.7*sigma
   A  79  LYS  CG
   A  79  LYS  CD          1.52     1.66    -0.14  3.00e-02  2.24e+01   4.7*sigma
   A  92  THR  CB
   A  92  THR  CG2         1.52     1.67    -0.15  3.30e-02  2.15e+01   4.6*sigma
   A  95  ASP  N
   A  95  ASP  CA          1.46     1.55    -0.09  1.90e-02  2.14e+01   4.6*sigma
   A  79  LYS  CB
   A  79  LYS  CG          1.52     1.66    -0.14  3.00e-02  2.12e+01   4.6*sigma
   A  78  ILE  N
   A  78  ILE  CA          1.46     1.37     0.09  1.90e-02  2.10e+01   4.6*sigma
   A 121  GLY  C
   A 122  ILE  N           1.33     1.39    -0.06  1.40e-02  1.99e+01   4.5*sigma
   A  88  ASP  C
   A  89  TYR  N           1.33     1.39    -0.06  1.40e-02  1.90e+01   4.4*sigma
   A 119  LEU  CA
   A 119  LEU  C           1.52     1.62    -0.09  2.10e-02  1.85e+01   4.3*sigma
   A 128  MET  N
   A 128  MET  CA          1.46     1.38     0.08  1.90e-02  1.85e+01   4.3*sigma
   A  83  THR  CB
   A  83  THR  OG1         1.43     1.37     0.07  1.60e-02  1.80e+01   4.2*sigma
   A 125  LYS  N
   A 125  LYS  CA          1.46     1.54    -0.08  1.90e-02  1.79e+01   4.2*sigma
   A 128  MET  CA
   A 128  MET  C           1.52     1.61    -0.09  2.10e-02  1.67e+01   4.1*sigma
   A  89  TYR  C
   A  90  SER  N           1.33     1.39    -0.06  1.40e-02  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.287 (Z= 15.102)
  Mean delta:    0.032 (Z=  1.612)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  O
   A 124  ALA  C
   A 125  LYS  N         123.00    65.56    57.44  1.60e+00  1.29e+03  35.9*sigma
   A  92  THR  OG1
   A  92  THR  CB
   A  92  THR  CG2       109.30    41.87    67.43  2.00e+00  1.14e+03  33.7*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O         120.80    82.78    38.02  1.70e+00  5.00e+02  22.4*sigma
   A  93  LEU  CD1
   A  93  LEU  CG
   A  93  LEU  CD2       110.80    69.24    41.56  2.20e+00  3.57e+02  18.9*sigma
   A  90  SER  N
   A  90  SER  CA
   A  90  SER  CB        110.50   142.02   -31.52  1.70e+00  3.44e+02  18.5*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  CG2       110.50   141.74   -31.24  1.70e+00  3.38e+02  18.4*sigma
   A  92  THR  CA
   A  92  THR  CB
   A  92  THR  OG1       109.60   132.43   -22.83  1.50e+00  2.32e+02  15.2*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N         116.20   145.90   -29.70  2.00e+00  2.21e+02  14.8*sigma
   A  89  TYR  C
   A  89  TYR  CA
   A  89  TYR  CB        110.10   137.45   -27.35  1.90e+00  2.07e+02  14.4*sigma
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        121.70   146.82   -25.12  1.80e+00  1.95e+02  14.0*sigma
   A  79  LYS  C
   A  79  LYS  CA
   A  79  LYS  CB        110.10    85.44    24.66  1.90e+00  1.68e+02  13.0*sigma
   A 131  ILE  CA
   A 131  ILE  CB
   A 131  ILE  CG1       110.40   132.39   -21.99  1.70e+00  1.67e+02  12.9*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  C         111.00   146.36   -35.36  2.80e+00  1.59e+02  12.6*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N         116.20    91.24    24.96  2.00e+00  1.56e+02  12.5*sigma
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   143.97   -22.27  1.80e+00  1.53e+02  12.4*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  CB        110.50   131.09   -20.59  1.70e+00  1.47e+02  12.1*sigma
   A 122  ILE  C
   A 122  ILE  CA
   A 122  ILE  CB        111.60   135.16   -23.56  2.00e+00  1.39e+02  11.8*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O         120.80   139.83   -19.03  1.70e+00  1.25e+02  11.2*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  C         111.00    79.74    31.26  2.80e+00  1.25e+02  11.2*sigma
   A  79  LYS  O
   A  79  LYS  C
   A  80  GLY  N         123.00   105.34    17.66  1.60e+00  1.22e+02  11.0*sigma
   A 121  GLY  O
   A 121  GLY  C
   A 122  ILE  N         123.00   105.40    17.60  1.60e+00  1.21e+02  11.0*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  CB        110.50    92.28    18.22  1.70e+00  1.15e+02  10.7*sigma
   A  78  ILE  CA
   A  78  ILE  CB
   A  78  ILE  CG1       110.40   128.46   -18.06  1.70e+00  1.13e+02  10.6*sigma
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        121.70   140.60   -18.90  1.80e+00  1.10e+02  10.5*sigma
   A 123  GLU  C
   A 123  GLU  CA
   A 123  GLU  CB        110.10   130.02   -19.92  1.90e+00  1.10e+02  10.5*sigma
   A 129  ARG  N
   A 129  ARG  CA
   A 129  ARG  CB        110.50   127.74   -17.24  1.70e+00  1.03e+02  10.1*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   103.50    18.20  1.80e+00  1.02e+02  10.1*sigma
   A  74  ASP  C
   A  74  ASP  CA
   A  74  ASP  CB        110.10   129.05   -18.95  1.90e+00  9.95e+01  10.0*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N         116.20   136.05   -19.85  2.00e+00  9.85e+01   9.9*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   139.32   -17.62  1.80e+00  9.58e+01   9.8*sigma
   A  79  LYS  N
   A  79  LYS  CA
   A  79  LYS  C         111.00    83.95    27.05  2.80e+00  9.33e+01   9.7*sigma
   A 122  ILE  CA
   A 122  ILE  CB
   A 122  ILE  CG1       110.40   126.10   -15.70  1.70e+00  8.53e+01   9.2*sigma
   A  79  LYS  CA
   A  79  LYS  CB
   A  79  LYS  CG        114.10   132.41   -18.31  2.00e+00  8.38e+01   9.2*sigma
   A  95  ASP  N
   A  95  ASP  CA
   A  95  ASP  CB        110.50   126.04   -15.54  1.70e+00  8.35e+01   9.1*sigma
   A  92  THR  C
   A  92  THR  CA
   A  92  THR  CB        109.10   128.80   -19.70  2.20e+00  8.02e+01   9.0*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N         116.20   134.06   -17.86  2.00e+00  7.98e+01   8.9*sigma
   A  82  THR  N
   A  82  THR  CA
   A  82  THR  CB        111.50   126.58   -15.08  1.70e+00  7.87e+01   8.9*sigma
   A  76  SER  CA
   A  76  SER  C
   A  76  SER  O         120.80   105.74    15.06  1.70e+00  7.85e+01   8.9*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  CB        110.50    95.47    15.03  1.70e+00  7.82e+01   8.8*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N         116.20    98.67    17.53  2.00e+00  7.69e+01   8.8*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG1       110.40   124.71   -14.31  1.70e+00  7.08e+01   8.4*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N         116.20    99.40    16.80  2.00e+00  7.05e+01   8.4*sigma
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        121.70   106.58    15.12  1.80e+00  7.05e+01   8.4*sigma
   A  50  TYR  C
   A  51  ILE  N
   A  51  ILE  CA        121.70   136.57   -14.87  1.80e+00  6.83e+01   8.3*sigma
   A 130  SER  C
   A 130  SER  CA
   A 130  SER  CB        110.10    94.44    15.66  1.90e+00  6.80e+01   8.2*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1       120.80   108.68    12.12  1.50e+00  6.53e+01   8.1*sigma
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   136.00   -14.30  1.80e+00  6.32e+01   7.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 125  LYS  O         120.80   133.96   -13.16  1.70e+00  5.99e+01   7.7*sigma
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        121.70   108.02    13.68  1.80e+00  5.77e+01   7.6*sigma
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        121.70   108.16    13.54  1.80e+00  5.66e+01   7.5*sigma
   A 127  ARG  CB
   A 127  ARG  CG
   A 127  ARG  CD        111.30   128.59   -17.29  2.30e+00  5.65e+01   7.5*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40    99.16    11.24  1.50e+00  5.62e+01   7.5*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N         116.20   130.78   -14.58  2.00e+00  5.32e+01   7.3*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   125.77   -14.17  2.00e+00  5.02e+01   7.1*sigma
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        121.70   134.21   -12.51  1.80e+00  4.83e+01   7.0*sigma
   A  77  ILE  CA
   A  77  ILE  CB
   A  77  ILE  CG2       110.50   122.03   -11.53  1.70e+00  4.60e+01   6.8*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  C         111.00    92.32    18.68  2.80e+00  4.45e+01   6.7*sigma
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        121.70   133.63   -11.93  1.80e+00  4.39e+01   6.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 126  VAL  O         120.80   132.01   -11.21  1.70e+00  4.35e+01   6.6*sigma
   A  97  SER  C
   A  97  SER  CA
   A  97  SER  CB        110.10   122.62   -12.52  1.90e+00  4.35e+01   6.6*sigma
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        121.70   109.91    11.79  1.80e+00  4.29e+01   6.6*sigma
   A 123  GLU  N
   A 123  GLU  CA
   A 123  GLU  C         111.00    92.98    18.02  2.80e+00  4.14e+01   6.4*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   125.35   -11.45  1.80e+00  4.05e+01   6.4*sigma
   A 122  ILE  CB
   A 122  ILE  CG1
   A 122  ILE  CD1       113.80   127.15   -13.35  2.10e+00  4.04e+01   6.4*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   118.94    -6.34  1.00e+00  4.02e+01   6.3*sigma
   A  79  LYS  CD
   A  79  LYS  CE
   A  79  LYS  NZ        111.90   132.16   -20.26  3.20e+00  4.01e+01   6.3*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  91  TYR  O         120.80   110.05    10.75  1.70e+00  4.00e+01   6.3*sigma
   A  79  LYS  CB
   A  79  LYS  CG
   A  79  LYS  CD        111.30   125.81   -14.51  2.30e+00  3.98e+01   6.3*sigma
   A 128  MET  O
   A 128  MET  C
   A 129  ARG  N         123.00   112.98    10.02  1.60e+00  3.92e+01   6.3*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD2       120.80   111.55     9.25  1.50e+00  3.80e+01   6.2*sigma
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        121.70   132.76   -11.06  1.80e+00  3.78e+01   6.1*sigma
   A 127  ARG  CA
   A 127  ARG  CB
   A 127  ARG  CG        114.10   126.32   -12.22  2.00e+00  3.73e+01   6.1*sigma
   A 129  ARG  NE
   A 129  ARG  CZ
   A 129  ARG  NH2       119.20   113.78     5.42  9.00e-01  3.62e+01   6.0*sigma
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        121.70   132.49   -10.79  1.80e+00  3.59e+01   6.0*sigma
   A  51  ILE  CA
   A  51  ILE  CB
   A  51  ILE  CG1       110.40   120.57   -10.17  1.70e+00  3.58e+01   6.0*sigma
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        121.70   132.46   -10.76  1.80e+00  3.58e+01   6.0*sigma
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        121.70   132.40   -10.70  1.80e+00  3.54e+01   5.9*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   118.50    -5.90  1.00e+00  3.48e+01   5.9*sigma
   A  82  THR  CA
   A  82  THR  CB
   A  82  THR  CG2       110.50   120.48    -9.98  1.70e+00  3.45e+01   5.9*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N         116.20   104.49    11.71  2.00e+00  3.43e+01   5.9*sigma
   A 119  LEU  C
   A 119  LEU  CA
   A 119  LEU  CB        110.10    99.02    11.08  1.90e+00  3.40e+01   5.8*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  78  ILE  O         120.80   110.96     9.84  1.70e+00  3.35e+01   5.8*sigma
   A  91  TYR  N
   A  91  TYR  CA
   A  91  TYR  CB        110.50   120.14    -9.64  1.70e+00  3.22e+01   5.7*sigma
   A  93  LEU  CB
   A  93  LEU  CG
   A  93  LEU  CD2       110.70   127.44   -16.74  3.00e+00  3.11e+01   5.6*sigma
   A 131  ILE  N
   A 131  ILE  CA
   A 131  ILE  C         111.00    95.47    15.53  2.80e+00  3.08e+01   5.5*sigma
   A 125  LYS  C
   A 125  LYS  CA
   A 125  LYS  CB        110.10   120.56   -10.46  1.90e+00  3.03e+01   5.5*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   119.84    -9.34  1.70e+00  3.02e+01   5.5*sigma
   A 127  ARG  N
   A 127  ARG  CA
   A 127  ARG  C         111.00   126.16   -15.16  2.80e+00  2.93e+01   5.4*sigma
   A  22  PRO  N
   A  22  PRO  CA
   A  22  PRO  CB        103.00   108.88    -5.88  1.10e+00  2.86e+01   5.3*sigma
   A  89  TYR  O
   A  89  TYR  C
   A  90  SER  N         123.00   114.48     8.52  1.60e+00  2.83e+01   5.3*sigma
   A 120  GLU  C
   A 120  GLU  CA
   A 120  GLU  CB        110.10   120.18   -10.08  1.90e+00  2.82e+01   5.3*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N         116.20   105.79    10.41  2.00e+00  2.71e+01   5.2*sigma
   A 116  ASP  C
   A 116  ASP  CA
   A 116  ASP  CB        110.10   119.88    -9.78  1.90e+00  2.65e+01   5.1*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  CB        110.50   119.18    -8.68  1.70e+00  2.61e+01   5.1*sigma
   A 128  MET  N
   A 128  MET  CA
   A 128  MET  CB        110.50   119.13    -8.63  1.70e+00  2.57e+01   5.1*sigma
   A 113  LYS  CG
   A 113  LYS  CD
   A 113  LYS  CE        111.30   122.95   -11.65  2.30e+00  2.56e+01   5.1*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N         116.20   106.19    10.01  2.00e+00  2.51e+01   5.0*sigma
   A 119  LEU  N
   A 119  LEU  CA
   A 119  LEU  C         111.00   125.01   -14.01  2.80e+00  2.51e+01   5.0*sigma
   A 130  SER  N
   A 130  SER  CA
   A 130  SER  C         111.00   124.96   -13.96  2.80e+00  2.49e+01   5.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N         116.20   126.15    -9.95  2.00e+00  2.48e+01   5.0*sigma
   A 116  ASP  N
   A 116  ASP  CA
   A 116  ASP  CB        110.50   118.92    -8.42  1.70e+00  2.45e+01   5.0*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   124.78     6.42  1.30e+00  2.44e+01   4.9*sigma
   A 122  ILE  N
   A 122  ILE  CA
   A 122  ILE  CB        111.50   103.11     8.39  1.70e+00  2.43e+01   4.9*sigma
   A  88  ASP  O
   A  88  ASP  C
   A  89  TYR  N         123.00   115.25     7.75  1.60e+00  2.35e+01   4.8*sigma
   A 130  SER  CA
   A 130  SER  C
   A 130  SER  O         120.80   128.96    -8.16  1.70e+00  2.30e+01   4.8*sigma
   A  83  THR  CA
   A  83  THR  CB
   A  83  THR  CG2       110.50   118.65    -8.15  1.70e+00  2.30e+01   4.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N         116.20   106.63     9.57  2.00e+00  2.29e+01   4.8*sigma
   A 128  MET  C
   A 128  MET  CA
   A 128  MET  CB        110.10   101.04     9.06  1.90e+00  2.27e+01   4.8*sigma
   A 120  GLU  CA
   A 120  GLU  CB
   A 120  GLU  CG        114.10   123.55    -9.45  2.00e+00  2.23e+01   4.7*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N         116.20   125.61    -9.41  2.00e+00  2.22e+01   4.7*sigma
   A 118  ASP  C
   A 118  ASP  CA
   A 118  ASP  CB        110.10   119.02    -8.92  1.90e+00  2.20e+01   4.7*sigma
   A  74  ASP  N
   A  74  ASP  CA
   A  74  ASP  CB        110.50   102.54     7.96  1.70e+00  2.19e+01   4.7*sigma
   A 126  VAL  C
   A 126  VAL  CA
   A 126  VAL  CB        111.40   102.55     8.85  1.90e+00  2.17e+01   4.7*sigma
   A  78  ILE  C
   A  78  ILE  CA
   A  78  ILE  CB        111.60   120.90    -9.30  2.00e+00  2.16e+01   4.7*sigma
   A  88  ASP  N
   A  88  ASP  CA
   A  88  ASP  CB        110.50   102.63     7.87  1.70e+00  2.14e+01   4.6*sigma
   A 114  PRO  N
   A 114  PRO  CA
   A 114  PRO  CB        103.00   108.09    -5.09  1.10e+00  2.14e+01   4.6*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N         116.20   106.97     9.23  2.00e+00  2.13e+01   4.6*sigma
   A  82  THR  CA
   A  82  THR  CB
   A  82  THR  OG1       109.60   116.44    -6.84  1.50e+00  2.08e+01   4.6*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N         116.20   107.09     9.11  2.00e+00  2.08e+01   4.6*sigma
   A 125  LYS  N
   A 125  LYS  CA
   A 125  LYS  C         111.00    98.36    12.64  2.80e+00  2.04e+01   4.5*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N         116.90   123.56    -6.66  1.50e+00  1.97e+01   4.4*sigma
   A  43  HIS  CB
   A  43  HIS  CG
   A  43  HIS  CD2       131.20   125.46     5.74  1.30e+00  1.95e+01   4.4*sigma
   A  51  ILE  N
   A  51  ILE  CA
   A  51  ILE  C         111.00   123.36   -12.36  2.80e+00  1.95e+01   4.4*sigma
   A  76  SER  CA
   A  76  SER  CB
   A  76  SER  OG        111.10   119.92    -8.82  2.00e+00  1.94e+01   4.4*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   116.99    -4.39  1.00e+00  1.93e+01   4.4*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N         116.20   107.44     8.76  2.00e+00  1.92e+01   4.4*sigma
   A  25  LEU  N
   A  25  LEU  CA
   A  25  LEU  CB        110.50   103.14     7.36  1.70e+00  1.87e+01   4.3*sigma
   A  70  LEU  CA
   A  70  LEU  C
   A  70  LEU  O         120.80   113.53     7.27  1.70e+00  1.83e+01   4.3*sigma
   A 124  ALA  C
   A 124  ALA  CA
   A 124  ALA  CB        110.50   116.92    -6.42  1.50e+00  1.83e+01   4.3*sigma
   A 127  ARG  C
   A 127  ARG  CA
   A 127  ARG  CB        110.10   101.98     8.12  1.90e+00  1.83e+01   4.3*sigma
   A 120  GLU  N
   A 120  GLU  CA
   A 120  GLU  C         111.00   122.87   -11.87  2.80e+00  1.80e+01   4.2*sigma
   A 123  GLU  CA
   A 123  GLU  CB
   A 123  GLU  CG        114.10   122.56    -8.46  2.00e+00  1.79e+01   4.2*sigma
   A 123  GLU  O
   A 123  GLU  C
   A 124  ALA  N         123.00   129.73    -6.73  1.60e+00  1.77e+01   4.2*sigma
   A 126  VAL  CG1
   A 126  VAL  CB
   A 126  VAL  CG2       110.80   101.54     9.26  2.20e+00  1.77e+01   4.2*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   118.04    -7.94  1.90e+00  1.75e+01   4.2*sigma
   A  74  ASP  O
   A  74  ASP  C
   A  75  GLU  N         123.00   116.39     6.61  1.60e+00  1.71e+01   4.1*sigma
   A  83  THR  OG1
   A  83  THR  CB
   A  83  THR  CG2       109.30   101.08     8.22  2.00e+00  1.69e+01   4.1*sigma
   A  15  PHE  CA
   A  15  PHE  CB
   A  15  PHE  CG        113.80   109.69     4.11  1.00e+00  1.69e+01   4.1*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.92     5.28  1.30e+00  1.65e+01   4.1*sigma
   A  15  PHE  CE1
   A  15  PHE  CZ
   A  15  PHE  CE2       120.00   127.30    -7.30  1.80e+00  1.65e+01   4.1*sigma
   A 126  VAL  N
   A 126  VAL  CA
   A 126  VAL  CB        111.50   104.61     6.89  1.70e+00  1.64e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.56     4.04  1.00e+00  1.63e+01   4.0*sigma
   A  86  ILE  N
   A  86  ILE  CA
   A  86  ILE  C         111.00   122.29   -11.29  2.80e+00  1.63e+01   4.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N         116.20   108.14     8.06  2.00e+00  1.62e+01   4.0*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.62e+01   4.0*sigma
   A  71  ILE  CA
   A  71  ILE  CB
   A  71  ILE  CG1       110.40   117.23    -6.83  1.70e+00  1.62e+01   4.0*sigma
   A 128  MET  CA
   A 128  MET  CB
   A 128  MET  CG        114.10   122.11    -8.01  2.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   67.426 (Z= 35.902)
  Mean delta:    5.692 (Z=  3.025)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00    60.50   119.50  5.00e+00  5.71e+02  23.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   -62.13  -117.87  5.00e+00  5.56e+02  23.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00    66.91   113.09  5.00e+00  5.12e+02  22.6*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00    76.38   103.62  5.00e+00  4.29e+02  20.7*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   100.35    79.65  5.00e+00  2.54e+02  15.9*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   101.18    78.82  5.00e+00  2.49e+02  15.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00  -103.09   -76.91  5.00e+00  2.37e+02  15.4*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   104.50    75.50  5.00e+00  2.28e+02  15.1*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00  -112.42   -67.58  5.00e+00  1.83e+02  13.5*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   124.36    55.64  5.00e+00  1.24e+02  11.1*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  78  ILE  N
   A  78  ILE  CA        180.00  -126.60   -53.40  5.00e+00  1.14e+02  10.7*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   129.21    50.79  5.00e+00  1.03e+02  10.2*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   129.29    50.71  5.00e+00  1.03e+02  10.1*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00  -133.32   -46.68  5.00e+00  8.72e+01   9.3*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -133.45   -46.55  5.00e+00  8.67e+01   9.3*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00  -134.03   -45.97  5.00e+00  8.45e+01   9.2*sigma
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -138.40   -41.60  5.00e+00  6.92e+01   8.3*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00   139.59    40.41  5.00e+00  6.53e+01   8.1*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00  -141.11   -38.89  5.00e+00  6.05e+01   7.8*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -141.48   -38.52  5.00e+00  5.94e+01   7.7*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   143.65    36.35  5.00e+00  5.28e+01   7.3*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   144.54    35.46  5.00e+00  5.03e+01   7.1*sigma
   A  73  GLY  CA
   A  73  GLY  C
   A  74  ASP  N
   A  74  ASP  CA        180.00  -144.90   -35.10  5.00e+00  4.93e+01   7.0*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   145.68    34.32  5.00e+00  4.71e+01   6.9*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   146.16    33.84  5.00e+00  4.58e+01   6.8*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   150.28    29.72  5.00e+00  3.53e+01   5.9*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -153.78   -26.22  5.00e+00  2.75e+01   5.2*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -154.87   -25.13  5.00e+00  2.53e+01   5.0*sigma
   A  75  GLU  CA
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        180.00   157.56    22.44  5.00e+00  2.01e+01   4.5*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   159.55    20.45  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.075
  Max. delta:  119.502
  Mean delta:   23.371

                       ----------Chiral volumes----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  N
   A  79  LYS  C
   A  79  LYS  CB          2.51    -4.46     6.98  2.00e-01  1.22e+03  34.9*sigma
   A 123  GLU  CA
   A 123  GLU  N
   A 123  GLU  C
   A 123  GLU  CB          2.51    -2.77     5.28  2.00e-01  6.96e+02  26.4*sigma
   A 124  ALA  CA
   A 124  ALA  N
   A 124  ALA  C
   A 124  ALA  CB          2.48    -2.70     5.19  2.00e-01  6.72e+02  25.9*sigma
   A 122  ILE  CB
   A 122  ILE  CA
   A 122  ILE  CG1
   A 122  ILE  CG2         2.64    -1.92     4.57  2.00e-01  5.21e+02  22.8*sigma
   A  78  ILE  CB
   A  78  ILE  CA
   A  78  ILE  CG1
   A  78  ILE  CG2         2.64    -1.63     4.27  2.00e-01  4.56e+02  21.4*sigma
   A  92  THR  CB
   A  92  THR  CA
   A  92  THR  OG1
   A  92  THR  CG2         2.55    -1.48     4.03  2.00e-01  4.06e+02  20.2*sigma
   A  78  ILE  CA
   A  78  ILE  N
   A  78  ILE  C
   A  78  ILE  CB          2.43    -1.45     3.88  2.00e-01  3.76e+02  19.4*sigma
   A  88  ASP  CA
   A  88  ASP  N
   A  88  ASP  C
   A  88  ASP  CB          2.51    -1.19     3.70  2.00e-01  3.43e+02  18.5*sigma
   A  51  ILE  CA
   A  51  ILE  N
   A  51  ILE  C
   A  51  ILE  CB          2.43    -1.06     3.50  2.00e-01  3.05e+02  17.5*sigma
   A 120  GLU  CA
   A 120  GLU  N
   A 120  GLU  C
   A 120  GLU  CB          2.51    -0.86     3.37  2.00e-01  2.83e+02  16.8*sigma
   A  97  SER  CA
   A  97  SER  N
   A  97  SER  C
   A  97  SER  CB          2.51    -0.69     3.20  2.00e-01  2.56e+02  16.0*sigma
   A 127  ARG  CA
   A 127  ARG  N
   A 127  ARG  C
   A 127  ARG  CB          2.51     0.51     2.00  2.00e-01  1.00e+02  10.0*sigma
   A 116  ASP  CA
   A 116  ASP  N
   A 116  ASP  C
   A 116  ASP  CB          2.51     1.03     1.48  2.00e-01  5.46e+01   7.4*sigma
   A  92  THR  CA
   A  92  THR  N
   A  92  THR  C
   A  92  THR  CB          2.53     1.11     1.42  2.00e-01  5.01e+01   7.1*sigma
   A  90  SER  CA
   A  90  SER  N
   A  90  SER  C
   A  90  SER  CB          2.51     1.12     1.39  2.00e-01  4.80e+01   6.9*sigma
   A  89  TYR  CA
   A  89  TYR  N
   A  89  TYR  C
   A  89  TYR  CB          2.51     1.18     1.33  2.00e-01  4.45e+01   6.7*sigma
   A  93  LEU  CG
   A  93  LEU  CB
   A  93  LEU  CD1
   A  93  LEU  CD2        -2.59    -3.52     0.93  2.00e-01  2.16e+01   4.6*sigma
   A  77  ILE  CB
   A  77  ILE  CA
   A  77  ILE  CG1
   A  77  ILE  CG2         2.64     1.76     0.88  2.00e-01  1.94e+01   4.4*sigma

  Min. delta:    0.002
  Max. delta:    6.975
  Mean delta:    1.171

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.569       0.591     6485.73  29.5*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 127  ARG  O
   A 128  MET  N             0.104       0.180      108.28   9.0*sigma
   A  77  ILE  CA
   A  77  ILE  C
   A  77  ILE  O
   A  78  ILE  N             0.091       0.156       82.17   7.8*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.089       0.132      158.18   6.6*sigma
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.072       0.130      103.80   6.5*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 123  GLU  O
   A 124  ALA  N             0.065       0.112       42.38   5.6*sigma
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.089       0.108      157.35   5.4*sigma
   A  92  THR  CA
   A  92  THR  C
   A  92  THR  O
   A  93  LEU  N             0.061       0.106       37.36   5.3*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  ND1
   A 135  HIS  CD2
   A 135  HIS  CE1
   A 135  HIS  NE2           0.079       0.097       93.26   4.9*sigma
   A 127  ARG  CD
   A 127  ARG  NE
   A 127  ARG  CZ
   A 127  ARG  NH1
   A 127  ARG  NH2           0.201       0.445       33.46   4.7*sigma
   A  67  PHE  CB
   A  67  PHE  CG
   A  67  PHE  CD1
   A  67  PHE  CD2
   A  67  PHE  CE1
   A  67  PHE  CE2
   A  67  PHE  CZ            0.058       0.085       58.19   4.3*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 124  ALA  O
   A 125  LYS  N             0.075       0.082       56.42   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.569
  Mean delta:    0.051

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    1" pdbres="HIS A  43  conformer  : HE2, HD1 
    1" pdbres="THR A  92  conformer  : HG1 
    1" pdbres="HIS A 134  conformer  : HE2, HD1 
    1" pdbres="HIS A 135  conformer  : HE2, HD1 
    1" pdbres="HIS A 136  conformer  : HE2, HD1 
    1" pdbres="HIS A 137  conformer  : HE2, HD1 
    1" pdbres="HIS A 138  conformer  : HE2, HD1 
    1" pdbres="HIS A 139  conformer  : HE2, HD1 

                       ----------Angle outliers----------                      

   A  77  ILE  HA , Angle N-CA-HA, observed: 122.024, delta from target: -12.024
   A  82  THR  HA , Angle CB-CA-HA, observed: 96.904, delta from target: 12.096
   A  86  ILE  HA , Angle N-CA-HA, observed: 97.721, delta from target: 12.279
   A  78  ILE  HB , Angle CG1-CB-HB, observed: 96.342, delta from target: 12.658
   A 131  ILE  HA , Angle N-CA-HA, observed: 122.724, delta from target: -12.724
   A  97  SER  HA , Angle C-CA-HA, observed: 96.209, delta from target: 12.791
   A 118  ASP  HA , Angle CB-CA-HA, observed: 96.137, delta from target: 12.863
   A  82  THR  HA , Angle C-CA-HA, observed: 122.022, delta from target: -13.022
   A  89  TYR  H  , Angle C-N-H, observed: 110.855, delta from target: 13.445
   A  74  ASP  HA , Angle N-CA-HA, observed: 123.469, delta from target: -13.469
   A 129  ARG  HA , Angle C-CA-HA, observed: 122.669, delta from target: -13.669
   A  77  ILE  HA , Angle CB-CA-HA, observed: 95.303, delta from target: 13.697
   A  51  ILE  HB , Angle CA-CB-HB, observed: 94.801, delta from target: 14.199
   A 129  ARG  HA , Angle N-CA-HA, observed: 94.926, delta from target: 15.074
   A  82  THR  HB , Angle CA-CB-HB, observed: 93.499, delta from target: 15.501
   A  51  ILE  HA , Angle C-CA-HA, observed: 93.438, delta from target: 15.562
   A 116  ASP  HA , Angle CB-CA-HA, observed: 93.056, delta from target: 15.944
   A 122  ILE  HA , Angle CB-CA-HA, observed: 93.018, delta from target: 15.982
   A 119  LEU  HA , Angle CB-CA-HA, observed: 125.909, delta from target: -16.909
   A 131  ILE  HB , Angle CG2-CB-HB, observed: 126.683, delta from target: -17.683
   A  92  THR  HA , Angle C-CA-HA, observed: 91.262, delta from target: 17.738
   A  95  ASP  HA , Angle N-CA-HA, observed: 92.258, delta from target: 17.742
   A 128  MET  HA , Angle C-CA-HA, observed: 127.939, delta from target: -17.939
   A  93  LEU  HG , Angle CD2-CG-HG, observed: 126.086, delta from target: -18.086
   A 125  LYS  HA , Angle N-CA-HA, observed: 128.261, delta from target: -18.261
   A  74  ASP  HA , Angle C-CA-HA, observed: 90.510, delta from target: 18.490
   A  89  TYR  HA , Angle CB-CA-HA, observed: 90.455, delta from target: 18.545
   A  78  ILE  HA , Angle C-CA-HA, observed: 90.010, delta from target: 18.990
   A 122  ILE  HB , Angle CA-CB-HB, observed: 89.357, delta from target: 19.643
   A  51  ILE  HA , Angle N-CA-HA, observed: 88.699, delta from target: 21.301
   A  93  LEU  HG , Angle CB-CG-HG, observed: 87.691, delta from target: 21.309
   A 131  ILE  HB , Angle CA-CB-HB, observed: 87.586, delta from target: 21.414
   A  78  ILE  HB , Angle CA-CB-HB, observed: 86.949, delta from target: 22.051
   A  90  SER  HA , Angle N-CA-HA, observed: 87.193, delta from target: 22.807
   A 127  ARG  HA , Angle C-CA-HA, observed: 132.335, delta from target: -23.335
   A 130  SER  HA , Angle N-CA-HA, observed: 85.931, delta from target: 24.069
   A  88  ASP  HA , Angle N-CA-HA, observed: 85.176, delta from target: 24.824
   A  79  LYS  HA , Angle C-CA-HA, observed: 134.215, delta from target: -25.215
   A  89  TYR  HA , Angle N-CA-HA, observed: 136.508, delta from target: -26.508
   A  92  THR  HA , Angle CB-CA-HA, observed: 82.112, delta from target: 26.888
   A 123  GLU  HA , Angle N-CA-HA, observed: 137.273, delta from target: -27.273
   A  97  SER  HA , Angle CB-CA-HA, observed: 81.083, delta from target: 27.917
   A  93  LEU  HG , Angle CD1-CG-HG, observed: 135.935, delta from target: -27.935
   A 120  GLU  HA , Angle C-CA-HA, observed: 80.904, delta from target: 28.096
   A  88  ASP  HA , Angle C-CA-HA, observed: 80.854, delta from target: 28.146
   A  77  ILE  HB , Angle CA-CB-HB, observed: 79.762, delta from target: 29.238
   A  90  SER  HA , Angle CB-CA-HA, observed: 77.796, delta from target: 31.204
   A 122  ILE  HA , Angle N-CA-HA, observed: 141.356, delta from target: -31.356
   A  92  THR  HB , Angle CG2-CB-HB, observed: 139.989, delta from target: -31.989
   A  89  TYR  HA , Angle C-CA-HA, observed: 76.245, delta from target: 32.755
   A  90  SER  HA , Angle C-CA-HA, observed: 143.367, delta from target: -34.367
   A  88  ASP  HA , Angle CB-CA-HA, observed: 148.331, delta from target: -39.331
   A  92  THR  HB , Angle OG1-CB-HB, observed: 148.671, delta from target: -39.671
   A  92  THR  HB , Angle CA-CB-HB, observed: 68.444, delta from target: 40.556
   A 127  ARG  HA , Angle N-CA-HA, observed: 34.600, delta from target: 75.400

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.023   0.287   2241  Z= 1.148
    Angle     :  4.847  75.400   4078  Z= 2.169
    Chirality :  1.171   6.975    176
    Planarity :  0.041   0.572    327
    Dihedral  : 18.601 119.502    768
    Min Nonbonded Distance : 1.159
  
  Molprobity Statistics.
    All-atom Clashscore : 64.50
    Ramachandran Plot:
      Outliers : 13.14 %
      Allowed  :  8.03 %
      Favored  : 78.83 %
    Rotamer:
      Outliers : 13.71 %
      Allowed  :  3.23 %
      Favored  : 83.06 %
    Cbeta Deviations : 21.97 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 28.57 %
      Twisted General : 17.56 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -3.06 (0.67), residues: 137
    helix: -1.21 (0.58), residues: 61
    sheet:  None (None), residues: 0
    loop : -2.86 (0.72), residues: 76
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.021   0.009   HIS A 135 
   PHE   0.276   0.064   PHE A  67 
   TYR   1.626   0.092   TYR A  89 
   ARG   0.140   0.028   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.021   0.009   HIS A 135 
   PHE   0.106   0.036   PHE A  67 
   TYR   1.233   0.096   TYR A  89 
   ARG   0.052   0.008   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  43  HIS

=================================== Summary ===================================

  Ramachandran outliers =  13.14 %
                favored =  78.83 %
  Rotamer outliers      =  13.71 %
  C-beta deviations     =    29
  Clashscore            =  64.50
  RMS(bonds)            =   0.0227
  RMS(angles)           =   4.85
  MolProbity score      =   3.90

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
