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


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


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


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


============================== 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)----------                  

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)----------                  

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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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 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: "   0"
    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)----------                  


  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   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: "   0"
    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}

  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  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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

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

  Time building chain proxies: 0.68, per 1000 atoms: 0.31
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (74.083, 48.814, 45.323, 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)----------                  


  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   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: "   0"
    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}

  Symmetric amino acids flipped
    None
  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: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.114, 77.429, 54.809, 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 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 ==============================


  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  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: "   0"
    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: (56.239, 55.022, 47.43, 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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      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 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  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: "   0"
    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: (43.214, 57.598, 61.158, 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 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: (45.068, 62.152, 47.764, 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: (60.755, 44.272, 51.125, 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   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: "   0"
    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}
Symmetry information was not found, putting molecule in P1 box.

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

        Number of residues, atoms: 139, 2224
          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: 1.01
  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.

        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: 61
        1.23 -     1.43: 411
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.36e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.24e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.44e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.25e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.90e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.87 -   105.66: 58
      105.66 -   111.46: 2416
      111.46 -   117.25: 571
      117.25 -   123.04: 814
      123.04 -   128.83: 220
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.50    4.10 1.00e+00 1.00e+00 1.68e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.69    4.51 1.30e+00 5.92e-01 1.21e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.01   -3.41 1.00e+00 1.00e+00 1.17e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.77    4.43 1.30e+00 5.92e-01 1.16e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.98   -3.38 1.00e+00 1.00e+00 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 973
       17.35 -    34.69: 38
       34.69 -    52.04: 14
       52.04 -    69.38: 5
       69.38 -    86.73: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" CB  ASP A 116 "
           model="   0" pdb=" CG  ASP A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.34   58.34     3      1.50e+01 4.44e-03 9.46e+00
  dihedral model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" CB  HIS A 137 "
           model="   0" pdb=" CG  HIS A 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.84   53.84     3      1.50e+01 4.44e-03 9.24e+00
  dihedral model="   0" pdb=" N   HIS A 136 "
           model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" CB  HIS A 136 "
           model="   0" pdb=" CG  HIS A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -127.14  -52.86     3      1.50e+01 4.44e-03 9.15e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 77
       0.046 -    0.091: 58
       0.091 -    0.137: 27
       0.137 -    0.182: 10
       0.182 -    0.228: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  GLU A  84 "
            model="   0" pdb=" N   GLU A  84 "
            model="   0" pdb=" C   GLU A  84 "
            model="   0" pdb=" CB  GLU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    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="   0" pdb=" CB  TYR A  81 "   -0.140 2.00e-02 2.50e+03   5.97e-02 1.07e+02
        model="   0" pdb=" CG  TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.115 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.032 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.075 2.00e-02 2.50e+03   3.33e-02 3.32e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.023 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.021 2.00e-02 2.50e+03   4.32e-02 1.86e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.075 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.026 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.18 -     1.87: 13
        1.87 -     2.55: 1860
        2.55 -     3.23: 6908
        3.23 -     3.92: 8043
        3.92 -     4.60: 12240
  Nonbonded interactions: 29064
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.184 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.579 1.850
  nonbonded model="   0" pdb=" HZ  PHE A  67 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.641 2.100
  nonbonded model="   0" pdb="HD12 ILE A  71 "
            model="   0" pdb=" OH  TYR A  81 "
     model   vdw
     1.683 2.620
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.696 1.850
  ... (remaining 29059 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: (51.318, 49.68, 48.231, 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: 2224
  At special positions: 0
  Unit cell: (67.731, 51.125, 51.977, 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    1113      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: (51.917, 44.071, 54.513, 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: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 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 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: "   0"
    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 -     1.04: 1106
        1.04 -     1.23: 95
        1.23 -     1.43: 377
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.57e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.68e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.25e+00
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.04e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 4.94e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.41 -   107.00: 276
      107.00 -   112.59: 2450
      112.59 -   118.18: 402
      118.18 -   123.78: 848
      123.78 -   129.37: 103
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   GLU A  49 "
        model="   0" pdb=" N   TYR A  50 "
        model="   0" pdb=" CA  TYR A  50 "
      ideal   model   delta    sigma   weight residual
     121.70  129.21   -7.51 1.80e+00 3.09e-01 1.74e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.30    4.90 1.30e+00 5.92e-01 1.42e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" ND1 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     122.70  128.18   -5.48 1.50e+00 4.44e-01 1.34e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.04    3.56 1.00e+00 1.00e+00 1.27e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.02   -4.62 1.40e+00 5.10e-01 1.09e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 974
       17.88 -    35.76: 48
       35.76 -    53.64: 8
       53.64 -    71.52: 2
       71.52 -    89.40: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A  48 "
           model="   0" pdb=" C   ALA A  48 "
           model="   0" pdb=" N   GLU A  49 "
           model="   0" pdb=" CA  GLU A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.17   30.83     0      5.00e+00 4.00e-02 3.80e+01
  dihedral model="   0" pdb=" CA  ASP A  47 "
           model="   0" pdb=" C   ASP A  47 "
           model="   0" pdb=" N   ALA A  48 "
           model="   0" pdb=" CA  ALA A  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.19  -18.81     0      5.00e+00 4.00e-02 1.42e+01
  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  163.35   16.65     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.052: 91
       0.052 -    0.102: 49
       0.102 -    0.153: 30
       0.153 -    0.203: 3
       0.203 -    0.254: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality model="   0" pdb=" CA  GLU A  49 "
            model="   0" pdb=" N   GLU A  49 "
            model="   0" pdb=" C   GLU A  49 "
            model="   0" pdb=" CB  GLU A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality model="   0" pdb=" CA  ALA A  48 "
            model="   0" pdb=" N   ALA A  48 "
            model="   0" pdb=" C   ALA A  48 "
            model="   0" pdb=" CB  ALA A  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.28    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.054 2.00e-02 2.50e+03   2.13e-02 1.36e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.050 2.00e-02 2.50e+03   1.92e-02 1.11e+01
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.047 2.00e-02 2.50e+03   1.79e-02 9.61e+00
        model="   0" pdb=" CG  TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.003 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 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 303
        2.28 -     2.86: 5096
        2.86 -     3.44: 5323
        3.44 -     4.02: 7022
        4.02 -     4.60: 10585
  Nonbonded interactions: 28329
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.701 1.850
  nonbonded model="   0" pdb="HG23 THR A  82 "
            model="   0" pdb=" HB3 SER A  90 "
     model   vdw
     1.714 2.440
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.749 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.796 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.799 1.850
  ... (remaining 28324 not shown)

  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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.479, 58.495, 67.203, 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: 1.02
  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.


  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: 1.11 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: 87
        1.23 -     1.43: 385
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.41e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.48e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.40e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.98e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.64e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.82 -   105.60: 55
      105.60 -   111.37: 2412
      111.37 -   117.15: 573
      117.15 -   122.93: 788
      122.93 -   128.70: 251
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.52    4.08 1.00e+00 1.00e+00 1.67e+01
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  128.11   -6.41 1.80e+00 3.09e-01 1.27e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.06    3.54 1.00e+00 1.00e+00 1.25e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.64    4.56 1.30e+00 5.92e-01 1.23e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.85   -3.25 1.00e+00 1.00e+00 1.06e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 972
       17.48 -    34.96: 39
       34.96 -    52.43: 16
       52.43 -    69.91: 3
       69.91 -    87.39: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  85 "
           model="   0" pdb=" C   LYS A  85 "
           model="   0" pdb=" N   ILE A  86 "
           model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.59   23.41     0      5.00e+00 4.00e-02 2.19e+01
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.88   17.12     0      5.00e+00 4.00e-02 1.17e+01
  dihedral model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
           model="   0" pdb=" CB  HIS A 139 "
           model="   0" pdb=" CG  HIS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.58   57.58     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 68
       0.042 -    0.083: 54
       0.083 -    0.124: 30
       0.124 -    0.165: 20
       0.165 -    0.206: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.34e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.089 2.00e-02 2.50e+03   3.58e-02 3.85e+01
        model="   0" pdb=" CG  TYR A  81 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.062 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.074 2.00e-02 2.50e+03   3.18e-02 3.03e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.049 2.00e-02 2.50e+03   2.73e-02 2.24e+01
        model="   0" pdb=" CG  TYR A  91 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.033 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 184
        2.22 -     2.82: 45  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 122
        1.23 -     1.43: 350
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.286  0.044 1.30e-02 5.92e+03 1.15e+01
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.67e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.59e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.41e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.86e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.80 -   106.43: 127
      106.43 -   112.05: 2509
      112.05 -   117.67: 448
      117.67 -   123.29: 806
      123.29 -   128.91: 189
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" 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="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.85    3.75 1.00e+00 1.00e+00 1.40e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.62    4.58 1.30e+00 5.92e-01 1.24e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.10   -3.50 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.91   -4.51 1.40e+00 5.10e-01 1.04e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.18: 958
       15.18 -    30.36: 57
       30.36 -    45.53: 14
       45.53 -    60.71: 2
       60.71 -    75.89: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ARG A 127 "
           model="   0" pdb=" C   ARG A 127 "
           model="   0" pdb=" N   MET A 128 "
           model="   0" pdb=" CA  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.16   29.84     0      5.00e+00 4.00e-02 3.56e+01
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.18   25.82     0      5.00e+00 4.00e-02 2.67e+01
  dihedral model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" C   HIS A 137 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.12   23.88     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 72
       0.038 -    0.075: 46
       0.075 -    0.113: 31
       0.113 -    0.151: 23
   57
        2.82 -     3.41: 5992
        3.41 -     4.01: 7466
        4.01 -     4.60: 11049
  Nonbonded interactions: 29248
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.626 2.440
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.660 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.696 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.753 1.850
  ... (remaining 29243 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
    0.151 -    0.188: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.87e-01
  chirality model="   0" pdb=" CG  LEU A 132 "
            model="   0" pdb=" CB  LEU A 132 "
            model="   0" pdb=" CD1 LEU A 132 "
            model="   0" pdb=" CD2 LEU A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.95e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.06e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.023 2.00e-02 2.50e+03   4.60e-02 2.11e+01
        model="   0" pdb=" CG  ASP A  36 "    0.079 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.060 2.00e-02 2.50e+03   2.62e-02 2.06e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.058 2.00e-02 2.50e+03   2.39e-02 1.71e+01
        model="   0" pdb=" CG  TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.26: 248
        2.26 -     2.84: 4898
        2.84 -     3.43: 5534
        3.43 -     4.01: 7088
        4.01 -     4.60: 10646
  Nonbonded interactions: 28414
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.675 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A 113 "
            model="   0" pdb=" OE2 GLU A 120 "
     model   vdw
     1.743 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.745 1.850
  nonbonded model="   0" pdb=" HB3 HIS A  43 "
            model="   0" pdb=" HE3 LYS A 113 "
     model   vdw
     1.759 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.773 1.850
  ... (remaining 28409 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 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: "   0"
    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}

  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: 1.14 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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU   16": "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: "   0"
    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: 85
        1.23 -     1.43: 387
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 8.82e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.385 -0.031 1.10e-02 8.26e+03 7.94e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.72e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.64e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.20e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.74 -   105.90: 81
      105.90 -   112.07: 2555
      112.07 -   118.23: 485
      118.23 -   124.39: 882
      124.39 -   130.56: 76
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  130.56   -8.86 1.80e+00 3.09e-01 2.42e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.50    4.10 1.00e+00 1.00e+00 1.68e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.48   -3.88 1.00e+00 1.00e+00 1.50e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.27    4.93 1.30e+00 5.92e-01 1.44e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.32    4.88 1.30e+00 5.92e-01 1.41e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 970
       17.24 -    34.48: 42
       34.48 -    51.73: 18
       51.73 -    68.97: 2
       68.97 -    86.21: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.33   28.67     0      5.00e+00 4.00e-02 3.29e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      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="   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  161.72   18.28     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 79
       0.041 -    0.082: 37
       0.082 -    0.123: 38
       0.123 -    0.164: 18
       0.164 -    0.205: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  GLU A  84 "
            model="   0" pdb=" N   GLU A  84 "
            model="   0" pdb=" C   GLU A  84 "
            model="   0" pdb=" CB  GLU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.37e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.081 2.00e-02 2.50e+03   3.22e-02 3.11e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.063 2.00e-02 2.50e+03   2.70e-02 2.19e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.066 2.00e-02 2.50e+03   2.58e-02 2.00e+01
        model="   0" pdb=" CG  TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.015 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.021 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 "    0.010 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 76
        2.11 -     2.73: 3747
        2.73 -     3.36: 6172
        3.36 -     3.98: 7442
        3.98 -     4.60: 11194
  Nonbonded interactions: 28631
  Sorted by model distance:
  nonbonded model="   0" pdb="HD23 LEU A 119 "
            model="   0" pdb="HD12 ILE A 122 "
     model   vdw
     1.488 2.440
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.585 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.602 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.663 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.727 1.850
  ... (remaining 28626 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: 1.18 seconds

  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: 2218
  At special positions: 0
  Unit cell: (43.653, 69.045, 53.444, 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 ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 1
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.86e+00
  bond model="   0" pdb=" C   ILE A  51 "
       model="   0" pdb=" N   PRO A  52 "
    ideal  model  delta    sigma   weight residual
    1.341  1.320  0.021 1.60e-02 3.91e+03 1.65e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.50e+00
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.466  0.025 2.10e-02 2.27e+03 1.37e+00
  bond model="   0" pdb=" C   GLU A 120 "
       model="   0" pdb=" N   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.36e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.43 -   106.56: 47
      106.56 -   112.69: 2729
      112.69 -   118.82: 434
      118.82 -   124.94: 827
      124.94 -   131.07: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.91   -4.91 3.00e+00 1.11e-01 2.68e+00
  angle model="   0" pdb=" NE  ARG A 129 "
        model="   0" pdb=" CZ  ARG A 129 "
        model="   0" pdb=" NH1 ARG A 129 "
      ideal   model   delta    sigma   weight residual
     121.50  119.95    1.55 1.00e+00 1.00e+00 2.41e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  104.44    4.56 3.00e+00 1.11e-01 2.31e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  104.58    4.42 3.00e+00 1.11e-01 2.17e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.34   -4.34 3.00e+00 1.11e-01 2.09e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.70: 983
       14.70 -    29.40: 24
       29.40 -    44.10: 18
       44.10 -    58.80: 5
       58.80 -    73.50: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  75 "
           model="   0" pdb=" CG  GLU A  75 "
           model="   0" pdb=" CD  GLU A  75 "
           model="   0" pdb=" OE1 GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -73.50   73.50     1      3.00e+01 1.11e-03 7.64e+00
  dihedral model="   0" pdb=" CB  GLU A  84 "
           model="   0" pdb=" CG  GLU A  84 "
           model="   0" pdb=" CD  GLU A  84 "
           model="   0" pdb=" OE1 GLU A  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -58.42   58.42     1      3.00e+01 1.11e-03 5.08e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -111.23  -68.77     2      3.00e+01 1.11e-03 4.63e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 121
       0.028 -    0.055: 34
       0.055 -    0.082: 13
       0.082 -    0.110: 6
       0.110 -    0.137: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.70e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.34e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.84e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.013 5.00e-02 4.00e+02   1.92e-02 5.88e-01
        model="   0" pdb=" N   PRO A   6 "    0.033 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.010 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.011 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 "    0.007 2.00e-02 2.50e+03   5.28e-03 5.58e-01
        model="   0" pdb=" CG  HIS A 139 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 138 "   -0.008 2.00e-02 2.50e+03   5.22e-03 5.44e-01
        model="   0" pdb=" CG  HIS A 138 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 138 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 138 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 138 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 138 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 138 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 138 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 131
        2.18 -     2.78: 4616
        2.78 -     3.39: 5827
        3.39 -     3.99: 7465
        3.99 -     4.60: 11725
  Nonbonded interactions: 29764
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.571 1.850
  nonbonded model="   0" pdb="HH21 ARG A 129 "
            model="   0" pdb=" OE2 GLU A 133 "
     model   vdw
     1.629 1.850
  nonbonded model="   0" pdb=" HE1 HIS A 137 "
            model="   0" pdb=" NE2 HIS A 139 "
     model   vdw
     1.691 2.600
  nonbonded model="   0" pdb="HD12 ILE A  37 "
            model="   0" pdb="HD23 LEU A  61 "
     model   vdw
     1.720 2.440
  nonbonded model="   0" pdb=" H   ASP A  88 "
            model="   0" pdb=" OH  TYR A  91 "
     model   vdw
     1.725 1.850
  ... (remaining 29759 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: 1.12 seconds

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


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

  Histogram of bond lengths:
        0.84 -     1.03: 1113
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" CZ  ARG A 127 "
       model="   0" 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="   0" pdb=" NE  ARG A 129 "
       model="   0" 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="   0" pdb=" CZ  ARG A  58 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       56.25 -    71.26: 1
       71.26 -    86.28: 0
       86.28 -   101.29: 2
      101.29 -   116.30: 2997
      116.30 -   131.32: 1091
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   56.25   53.22 3.00e+00 1.11e-01 3.15e+02
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  131.32  -21.85 3.00e+00 1.11e-01 5.30e+01
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.17   -9.70 3.00e+00 1.11e-01 1.05e+01
  angle model="   0" pdb=" CA  GLY A  80 "
        model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" H   GLY A  80 "
      ideal   model   delta    sigma   weight residual
     114.00  119.94   -5.94 3.00e+00 1.11e-01 3.91e+00
  angle model="   0" pdb=" CA  GLY A  42 "
        model="   0" pdb=" N   GLY A  42 "
        model="   0" pdb=" H   GLY A  42 "
      ideal   model   delta    sigma   weight residual
     114.00  119.93   -5.93 3.00e+00 1.11e-01 3.90e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 789
       16.10 -    32.19: 109
       32.19 -    48.29: 84
       48.29 -    64.39: 44
       64.39 -    80.48: 13
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CB  ARG A  58 "
           model="   0" pdb=" CG  ARG A  58 "
           model="   0" pdb=" CD  ARG A  58 "
           model="   0" 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="   0" pdb=" CA  MET A 128 "
           model="   0" pdb=" CB  MET A 128 "
           model="   0" pdb=" CG  MET A 128 "
           model="   0" 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="   0" pdb=" CA  ARG A 129 "
           model="   0" pdb=" CB  ARG A 129 "
           model="   0" pdb=" CG  ARG A 129 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" 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="   0" pdb=" CA  ILE A  37 "
            model="   0" pdb=" N   ILE A  37 "
            model="   0" pdb=" C   ILE A  37 "
            model="   0" 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="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" 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="   0" pdb=" CB  TYR A 111 "   -0.000 2.00e-02 2.50e+03   5.18e-04 8.05e-03
        model="   0" pdb=" CG  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  45 "    0.000 2.00e-02 2.50e+03   4.92e-04 7.25e-03
        model="   0" pdb=" CG  PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  45 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.000 2.00e-02 2.50e+03   4.77e-04 6.82e-03
        model="   0" pdb=" CG  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.000 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.44: 1271
        2.44 -     2.98: 5166
        2.98 -     3.52: 5550
        3.52 -     4.06: 6900
        4.06 -     4.60: 9736
  Nonbonded interactions: 28623
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LEU A   9 "
            model="   0" pdb=" H   SER A  13 "
     model   vdw
     1.906 1.850
  nonbonded model="   0" pdb=" O   ILE A 108 "
            model="   0" pdb=" H   TYR A 111 "
     model   vdw
     1.915 1.850
  nonbonded model="   0" pdb=" O   GLU A  16 "
            model="   0" pdb=" H   THR A  20 "
     model   vdw
     1.917 1.850
  nonbonded model="   0" pdb=" O   PRO A 117 "
            model="   0" pdb=" H   LEU A 119 "
     model   vdw
     1.927 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.929 1.850
  ... (remaining 28618 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: 1.14 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: 67
        1.23 -     1.43: 405
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.61e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.32e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.80e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.96e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 5.13e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.87 -   106.46: 122
      106.46 -   112.04: 2516
      112.04 -   117.63: 439
      117.63 -   123.21: 811
      123.21 -   128.79: 191
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.78    3.82 1.00e+00 1.00e+00 1.46e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.15    3.45 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.82    4.38 1.30e+00 5.92e-01 1.14e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.90   -3.30 1.00e+00 1.00e+00 1.09e+01
  angle model="   0" pdb=" CA  ASP A  44 "
        model="   0" pdb=" CB  ASP A  44 "
        model="   0" pdb=" CG  ASP A  44 "
      ideal   model   delta    sigma   weight residual
     112.60  115.82   -3.22 1.00e+00 1.00e+00 1.04e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 970
       17.17 -    34.35: 47
       34.35 -    51.52: 9
       51.52 -    68.69: 4
       68.69 -    85.87: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.85   24.15     0      5.00e+00 4.00e-02 2.33e+01
  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  161.13   18.87     0      5.00e+00 4.00e-02 1.42e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.26  -18.74     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 83
       0.052 -    0.104: 59
       0.104 -    0.155: 31
       0.155 -    0.207: 2
       0.207 -    0.259: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.50e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.08e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.059 2.00e-02 2.50e+03   2.56e-02 1.96e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.012 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 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.065 2.00e-02 2.50e+03   2.56e-02 1.96e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.054 2.00e-02 2.50e+03   2.08e-02 1.30e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 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 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.09: 61
        2.09 -     2.72: 3634
        2.72 -     3.35: 6154
        3.35 -     3.97: 7457
        3.97 -     4.60: 11300
  Nonbonded interactions: 28606
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.467 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.704 1.850
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" HZ3 LYS A 125 "
     model   vdw
     1.722 2.270
  nonbonded model="   0" pdb=" OE2 GLU A   8 "
            model="   0" pdb="HH21 ARG A  58 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.742 1.850
  ... (remaining 28601 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}

  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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      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: 1.07
  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.

        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: 69
        1.23 -     1.43: 403
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.49e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.37e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.59e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.41e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.73e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.98 -   107.39: 427
      107.39 -   112.80: 2316
      112.80 -   118.20: 377
      118.20 -   123.61: 836
      123.61 -   129.02: 123
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.36   -3.76 1.00e+00 1.00e+00 1.42e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.90    3.70 1.00e+00 1.00e+00 1.37e+01
  angle model="   0" pdb=" CA  HIS A 135 "
        model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
      ideal   model   delta    sigma   weight residual
     113.80  110.15    3.65 1.00e+00 1.00e+00 1.33e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.17    3.43 1.00e+00 1.00e+00 1.17e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.79    4.41 1.30e+00 5.92e-01 1.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 977
       17.21 -    34.43: 42
       34.43 -    51.64: 8
       51.64 -    68.85: 5
       68.85 -    86.07: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.15  -22.85     0      5.00e+00 4.00e-02 2.09e+01
  dihedral model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" C   ASP A 116 "
           model="   0" pdb=" N   PRO A 117 "
           model="   0" pdb=" CA  PRO A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.62  -21.38     0      5.00e+00 4.00e-02 1.83e+01
  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  160.64   19.36     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 85
       0.046 -    0.092: 47
       0.092 -    0.139: 34
       0.139 -    0.185: 7
       0.185 -    0.231: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality model="   0" pdb=" CG  LEU A  39 "
            model="   0" pdb=" CB  LEU A  39 "
            model="   0" pdb=" CD1 LEU A  39 "
            model="   0" pdb=" CD2 LEU A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality model="   0" pdb=" CA  PRO A 117 "
            model="   0" pdb=" N   PRO A 117 "
            model="   0" pdb=" C   PRO A 117 "
            model="   0" pdb=" CB  PRO A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.78e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.076 2.00e-02 2.50e+03   3.04e-02 2.77e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.055 2.00e-02 2.50e+03   2.14e-02 1.38e+01
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.005 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 "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "    0.043 2.00e-02 2.50e+03   1.99e-02 1.18e+01
        model="   0" pdb=" CG  TYR A  68 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 73
        2.11 -     2.74: 3827
        2.74 -     3.36: 6109
        3.36 -     3.98: 7502
        3.98 -     4.60: 11434
  Nonbonded interactions: 28945
  Sorted by model distance:
  nonbonded model="   0" pdb="HD23 LEU A  39 "
            model="   0" pdb=" HB1 ALA A 124 "
     model   vdw
     1.493 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.514 1.850
  nonbonded model="   0" pdb=" OH  TYR A  68 "
            model="   0" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.611 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.721 1.850
  nonbonded model="   0" pdb=" HH  TYR A  68 "
            model="   0" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.736 2.100
  ... (remaining 28940 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: 2218
  At special positions: 0
  Unit cell: (48.955, 49.069, 49.283, 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.
  Time building chain proxies: 1.00, per 1000 atoms: 0.45
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (36.385, 47.334, 78.84, 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: 1.04
  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.

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.597, 97.35, 39.616, 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: 79
        1.23 -     1.43: 393
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.54e+00
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.288 -0.057 2.00e-02 2.50e+03 8.08e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.98e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.03e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.58e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.59 -   106.25: 99
      106.25 -   111.91: 2512
      111.91 -   117.58: 477
      117.58 -   123.24: 800
      123.24 -   128.90: 191
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 138 "
        model="   0" pdb=" CG  HIS A 138 "
        model="   0" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  126.17    5.03 1.30e+00 5.92e-01 1.50e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.96    3.64 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.59    4.61 1.30e+00 5.92e-01 1.26e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.85    4.35 1.30e+00 5.92e-01 1.12e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.90   -4.50 1.40e+00 5.10e-01 1.03e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 980
       16.92 -    33.85: 38
       33.85 -    50.77: 9
       50.77 -    67.70: 4
       67.70 -    84.62: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A 120 "
           model="   0" pdb=" C   GLU A 120 "
           model="   0" pdb=" N   GLY A 121 "
           model="   0" pdb=" CA  GLY A 121 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.14   22.86     0      5.00e+00 4.00e-02 2.09e+01
  dihedral model="   0" pdb=" CA  ILE A 122 "
           model="   0" pdb=" C   ILE A 122 "
           model="   0" pdb=" N   GLU A 123 "
           model="   0" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.72   22.28     0      5.00e+00 4.00e-02 1.99e+01
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.81   21.19     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.041: 81
       0.041 -    0.082: 53
       0.082 -    0.123: 26
       0.123 -    0.163: 12
       0.163 -    0.204: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality model="   0" pdb=" CB  THR A  83 "
            model="   0" pdb=" CA  THR A  83 "
            model="   0" pdb=" OG1 THR A  83 "
            model="   0" pdb=" CG2 THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.20 2.00e-01 2.50e+01 9.51e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.07e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.078 2.00e-02 2.50e+03   3.39e-02 3.45e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.060 2.00e-02 2.50e+03   2.39e-02 1.71e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.050 2.00e-02 2.50e+03   1.96e-02 1.15e+01
        model="   0" pdb=" CG  TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 164
        2.21 -     2.81: 4419
        2.81 -     3.40: 5868
        3.40 -     4.00: 7258
        4.00 -     4.60: 10819
  Nonbonded interactions: 28528
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.609 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.743 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.744 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.758 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A 109 "
            model="   0" pdb=" OD1 ASP A 110 "
     model   vdw
     1.769 1.850
  ... (remaining 28523 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2224
          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)----------                  

  Time building chain proxies: 0.72, per 1000 atoms: 0.32
  Number of scatterers: 2224
  At special positions: 0
  Unit cell: (50.877, 58.72, 52.248, 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     216      8.00
     N     180      7.00
     C     713      6.00
     H    1113      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: 1.06
  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 -     1.23: 52
        1.23 -     1.43: 420
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.37e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.97e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.67e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.06e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.03e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.73 -   106.74: 166
      106.74 -   112.75: 2563
      112.75 -   118.76: 457
      118.76 -   124.77: 831
      124.77 -   130.78: 62
  Bond angle restraints: 4079
  Sorted by residual:
  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  130.78   -9.08 1.80e+00 3.09e-01 2.54e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" 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
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.24    4.96 1.30e+00 5.92e-01 1.45e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.90    3.70 1.00e+00 1.00e+00 1.37e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.94    3.66 1.00e+00 1.00e+00 1.34e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.42: 964
       16.42 -    32.84: 46
       32.84 -    49.26: 19
       49.26 -    65.68: 2
       65.68 -    82.10: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.65  -24.35     0      5.00e+00 4.00e-02 2.37e+01
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.55  -23.45     0      5.00e+00 4.00e-02 2.20e+01
  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  159.21   20.79     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 86
       0.050 -    0.100: 52
       0.100 -    0.149: 34
       0.149 -    0.199: 2
       0.199 -    0.249: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality model="   0" pdb=" CA  ASP A 118 "
            model="   0" pdb=" N   ASP A 118 "
            model="   0" pdb=" C   ASP A 118 "
            model="   0" pdb=" CB  ASP A 118 "
    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="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.08e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.070 2.00e-02 2.50e+03   3.03e-02 2.75e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.060 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 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.063 2.00e-02 2.50e+03   2.55e-02 1.95e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.049 2.00e-02 2.50e+03   1.90e-02 1.09e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 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 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 377
        2.31 -     2.88: 5151
        2.88 -     3.45: 5415
        3.45 -     4.03: 7259
        4.03 -     4.60: 10525
  Nonbonded interactions: 28727
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.734 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.746 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.752 1.850
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.754 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.761 1.850
  ... (remaining 28722 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: 1.14 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 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: "   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: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.11 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...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.74 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: 94
        1.23 -     1.43: 378
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.86e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.99e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.78e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.74e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.32e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.17 -   105.94: 74
      105.94 -   111.71: 2498
      111.71 -   117.48: 485
      117.48 -   123.25: 835
      123.25 -   129.02: 187
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.37    4.23 1.00e+00 1.00e+00 1.79e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.59   -3.99 1.00e+00 1.00e+00 1.59e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.23   -3.63 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.52    4.68 1.30e+00 5.92e-01 1.29e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.88    4.32 1.30e+00 5.92e-01 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 970
       17.95 -    35.91: 45
       35.91 -    53.86: 15
       53.86 -    71.82: 2
       71.82 -    89.77: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.07   28.93     0      5.00e+00 4.00e-02 3.35e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.35   22.65     0      5.00e+00 4.00e-02 2.05e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.19   21.81     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 79
       0.041 -    0.082: 42
       0.082 -    0.123: 36
       0.123 -    0.164: 15
       0.164 -    0.205: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.68e-01
  chirality model="   0" pdb=" CG  LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
            model="   0" pdb=" CD1 LEU A  93 "
            model="   0" pdb=" CD2 LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.29e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.061 2.00e-02 2.50e+03   2.40e-02 1.72e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  PRO A 114 "    0.015 2.00e-02 2.50e+03   3.13e-02 9.81e+00
        model="   0" pdb=" C   PRO A 114 "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" O   PRO A 114 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" N   ALA A 115 "    0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.047 2.00e-02 2.50e+03   1.78e-02 9.51e+00
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.003 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 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.25: 239
        2.25 -     2.84: 4797
        2.84 -     3.43: 5673
        3.43 -     4.01: 7149
        4.01 -     4.60: 10821
  Nonbonded interactions: 28679
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.666 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.742 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.748 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.764 1.850
  nonbonded model="   0" pdb=" OH  TYR A  68 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.779 1.850
  ... (remaining 28674 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: 0.95
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.05 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: 4
        1.23 -     1.42: 461
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 137 "
       model="   0" pdb=" N   HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.329  1.304  0.025 1.40e-02 5.10e+03 3.16e+00
  bond model="   0" pdb=" C   HIS A 134 "
       model="   0" pdb=" N   HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.25e+00
  bond model="   0" pdb=" C   HIS A 136 "
       model="   0" pdb=" N   HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.20e+00
  bond model="   0" pdb=" C   GLU A 133 "
       model="   0" pdb=" N   HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.05e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" CD2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.354  1.342  0.012 1.10e-02 8.26e+03 1.18e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.91 -   106.94: 68
      106.94 -   112.96: 2708
      112.96 -   118.99: 433
      118.99 -   125.01: 827
      125.01 -   131.04: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.65    5.35 3.00e+00 1.11e-01 3.18e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.67    5.33 3.00e+00 1.11e-01 3.16e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.17   -5.17 3.00e+00 1.11e-01 2.97e+00
  angle model="   0" pdb=" C   PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  104.41    4.59 3.00e+00 1.11e-01 2.34e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.58   -4.58 3.00e+00 1.11e-01 2.33e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 996
       17.64 -    35.27: 19
       35.27 -    52.91: 13
       52.91 -    70.55: 2
       70.55 -    88.19: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.19   88.19     1      3.00e+01 1.11e-03 1.03e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -81.62   81.62     1      3.00e+01 1.11e-03 9.11e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -101.28  -78.72     2      3.00e+01 1.11e-03 5.13e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 107
       0.029 -    0.058: 44
       0.058 -    0.087: 20
       0.087 -    0.116: 3
       0.116 -    0.145: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.28e-01
  chirality model="   0" pdb=" CA  VAL A 112 "
            model="   0" pdb=" N   VAL A 112 "
            model="   0" pdb=" C   VAL A 112 "
            model="   0" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.16e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.00e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.012 2.00e-02 2.50e+03   6.17e-03 1.14e+00
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.013 2.00e-02 2.50e+03   6.05e-03 1.10e+00
        model="   0" pdb=" CG  TYR A  81 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.015 5.00e-02 4.00e+02   2.32e-02 8.62e-01
        model="   0" pdb=" N   PRO A   6 "    0.040 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.25 -     1.92: 17
        1.92 -     2.59: 2274
        2.59 -     3.26: 6761
        3.26 -     3.93: 7853
        3.93 -     4.60: 12239
  Nonbonded interactions: 29144
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ILE A  77 "
            model="   0" pdb=" HH  TYR A  91 "
     model   vdw
     1.247 1.850
  nonbonded model="   0" pdb=" HB2 TYR A  81 "
            model="   0" pdb=" HE1 TYR A  91 "
     model   vdw
     1.566 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.647 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  88 "
            model="   0" pdb=" HZ2 LYS A 101 "
     model   vdw
     1.660 1.850
  nonbonded model="   0" pdb=" HE1 TYR A  68 "
            model="   0" pdb="HG23 ILE A  86 "
     model   vdw
     1.736 2.270
  ... (remaining 29139 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: 1113
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" CZ  ARG A 127 "
       model="   0" 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="   0" pdb=" NE  ARG A  21 "
       model="   0" 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="   0" pdb=" CZ  ARG A  21 "
       model="   0" 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="   0" pdb=" CZ  ARG A  58 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       34.61 -    53.87: 1
       53.87 -    73.12: 0
       73.12 -    92.38: 1
       92.38 -   111.64: 2723
      111.64 -   130.89: 1366
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   34.61   74.86 3.00e+00 1.11e-01 6.23e+02
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   75.08   34.39 3.00e+00 1.11e-01 1.31e+02
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.15   -9.68 3.00e+00 1.11e-01 1.04e+01
  angle model="   0" pdb=" CA  GLY A  87 "
        model="   0" pdb=" N   GLY A  87 "
        model="   0" pdb=" H   GLY A  87 "
      ideal   model   delta    sigma   weight residual
     114.00  119.93   -5.93 3.00e+00 1.11e-01 3.91e+00
  angle model="   0" pdb=" CA  GLY A  94 "
        model="   0" pdb=" N   GLY A  94 "
        model="   0" pdb=" H   GLY A  94 "
      ideal   model   delta    sigma   weight residual
     114.00  119.90   -5.90 3.00e+00 1.11e-01 3.87e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 802
       17.91 -    35.83: 123
       35.83 -    53.74: 77
       53.74 -    71.65: 29
       71.65 -    89.56: 8
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A  44 "
           model="   0" pdb=" CB  ASP A  44 "
           model="   0" pdb=" CG  ASP A  44 "
           model="   0" 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="   0" pdb=" N   GLU A  32 "
           model="   0" pdb=" CA  GLU A  32 "
           model="   0" pdb=" CB  GLU A  32 "
           model="   0" 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="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" CB  ILE A  86 "
           model="   0" pdb=" CG1 ILE A  86 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" 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="   0" pdb=" CA  ILE A  30 "
            model="   0" pdb=" N   ILE A  30 "
            model="   0" pdb=" C   ILE A  30 "
            model="   0" 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="   0" pdb=" CA  ILE A  37 "
            model="   0" pdb=" N   ILE A  37 "
            model="   0" pdb=" C   ILE A  37 "
            model="   0" 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="   0" pdb=" CB  TYR A  12 "    0.000 2.00e-02 2.50e+03   6.03e-04 1.09e-02
        model="   0" pdb=" CG  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.000 2.00e-02 2.50e+03   5.62e-04 9.46e-03
        model="   0" pdb=" CG  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.000 2.00e-02 2.50e+03   5.53e-04 9.18e-03
        model="   0" pdb=" CG  TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.000 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.45: 1367
        2.45 -     2.99: 5128
        2.99 -     3.53: 5537
        3.53 -     4.06: 6922
        4.06 -     4.60: 9735
  Nonbonded interactions: 28689
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LEU A  26 "
            model="   0" pdb=" H   ILE A  30 "
     model   vdw
     1.917 1.850
  nonbonded model="   0" pdb=" HG1 THR A  56 "
            model="   0" pdb=" O   LEU A 107 "
     model   vdw
     1.920 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.929 1.850
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.951 1.850
  nonbonded model="   0" pdb=" O   LYS A 125 "
            model="   0" pdb=" H   ARG A 129 "
     model   vdw
     1.982 1.850
  ... (remaining 28684 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: 105
        1.23 -     1.43: 367
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.68e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.54e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.50e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.49e+00
  bond model="   0" pdb=" C   GLY A  80 "
       model="   0" pdb=" N   TYR A  81 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.40e-02 5.10e+03 5.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.17 -   106.69: 170
      106.69 -   112.20: 2471
      112.20 -   117.72: 457
      117.72 -   123.24: 774
      123.24 -   128.75: 207
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.53    4.67 1.30e+00 5.92e-01 1.29e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.58    4.62 1.30e+00 5.92e-01 1.26e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.17    3.43 1.00e+00 1.00e+00 1.18e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.86    4.34 1.30e+00 5.92e-01 1.11e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  115.90   -3.30 1.00e+00 1.00e+00 1.09e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.93: 959
       16.93 -    33.86: 57
       33.86 -    50.79: 12
       50.79 -    67.72: 3
       67.72 -    84.65: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ARG A 127 "
           model="   0" pdb=" C   ARG A 127 "
           model="   0" pdb=" N   MET A 128 "
           model="   0" pdb=" CA  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.87   32.13     0      5.00e+00 4.00e-02 4.13e+01
  dihedral model="   0" pdb=" CA  GLU A 133 "
           model="   0" pdb=" C   GLU A 133 "
           model="   0" pdb=" N   HIS A 134 "
           model="   0" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.23   30.77     0      5.00e+00 4.00e-02 3.79e+01
  dihedral model="   0" pdb=" CA  LEU A 132 "
           model="   0" pdb=" C   LEU A 132 "
           model="   0" pdb=" N   GLU A 133 "
           model="   0" pdb=" CA  GLU A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.72   29.28     0      5.00e+00 4.00e-02 3.43e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 75
       0.046 -    0.091: 52
       0.091 -    0.136: 38
       0.136 -    0.181: 9
       0.181 -    0.227: 2
  Chirality restraints: 176
  Sorted by residual:
  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    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.75e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.52e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.071 2.00e-02 2.50e+03   3.02e-02 2.73e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.065 2.00e-02 2.50e+03   2.59e-02 2.01e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.017 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        model="   0" pdb=" CG  ASP A  36 "    0.062 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 103
        2.15 -     2.76: 4006
        2.76 -     3.37: 6015
        3.37 -     3.99: 7191
        3.99 -     4.60: 10861
  Nonbonded interactions: 28176
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.534 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.692 1.850
  nonbonded model="   0" pdb=" HB  THR A  82 "
            model="   0" pdb=" HG3 GLU A  84 "
     model   vdw
     1.747 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.768 1.850
  ... (remaining 28171 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 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: "   0"
    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: 0.91, per 1000 atoms: 0.41
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (81.821, 46.815, 44.204, 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 ==============================

        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 ==============================

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (73.776, 44.503, 43.398, 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 ==============================


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


  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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      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: 1.15 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)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 43
        1.23 -     1.42: 429
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" 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
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.67e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.58e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.11e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.58e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.11 -   105.87: 72
      105.87 -   111.64: 2471
      111.64 -   117.40: 514
      117.40 -   123.16: 809
      123.16 -   128.92: 213
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.31    4.29 1.00e+00 1.00e+00 1.84e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.02    3.58 1.00e+00 1.00e+00 1.28e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.64    4.56 1.30e+00 5.92e-01 1.23e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.92   -4.52 1.40e+00 5.10e-01 1.04e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.81   -3.21 1.00e+00 1.00e+00 1.03e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 977
       17.39 -    34.77: 35
       34.77 -    52.16: 17
       52.16 -    69.55: 3
       69.55 -    86.94: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.65   21.35     0      5.00e+00 4.00e-02 1.82e+01
  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  161.43   18.57     0      5.00e+00 4.00e-02 1.38e+01
  dihedral model="   0" pdb=" CA  VAL A 112 "
           model="   0" pdb=" C   VAL A 112 "
           model="   0" pdb=" N   LYS A 113 "
           model="   0" pdb=" CA  LYS A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.52   16.48     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 74
       0.040 -    0.079: 47
       0.079 -    0.118: 29
       0.118 -    0.157: 22
       0.157 -    0.196: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.61e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.20e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.29e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.066 2.00e-02 2.50e+03   2.89e-02 2.50e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 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 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.064 2.00e-02 2.50e+03   2.50e-02 1.88e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.048 2.00e-02 2.50e+03   1.85e-02 1.02e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 340
        2.29 -     2.87: 5164
        2.87 -     3.45: 5503
        3.45 -     4.02: 7363
        4.02 -     4.60: 10811
  Nonbonded interactions: 29181
  Sorted by model distance:
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.713 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.742 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.747 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.779 1.850
  ... (remaining 29176 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: 1.05
  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.

        Number of residues, atoms: 139, 2224
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 59
        1.23 -     1.42: 413
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.59e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 5.11e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 4.93e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.91e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.76e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.09 -   105.95: 88
      105.95 -   111.82: 2502
      111.82 -   117.68: 488
      117.68 -   123.55: 860
      123.55 -   129.42: 141
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  129.42   -7.72 1.80e+00 3.09e-01 1.84e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.52    4.08 1.00e+00 1.00e+00 1.66e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.01    3.59 1.00e+00 1.00e+00 1.29e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.81    4.39 1.30e+00 5.92e-01 1.14e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.81   -4.41 1.40e+00 5.10e-01 9.91e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 971
       17.01 -    34.02: 42
       34.02 -    51.02: 16
       51.02 -    68.03: 2
       68.03 -    85.04: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  156.53   23.47     0      5.00e+00 4.00e-02 2.20e+01
  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  162.97   17.03     0      5.00e+00 4.00e-02 1.16e+01
  dihedral model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" C   ASP A 116 "
           model="   0" pdb=" N   PRO A 117 "
           model="   0" pdb=" CA  PRO A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.63  -16.37     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.041: 80
       0.041 -    0.082: 44
       0.082 -    0.123: 32
       0.123 -    0.164: 15
       0.164 -    0.204: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  THR A  83 "
            model="   0" pdb=" N   THR A  83 "
            model="   0" pdb=" C   THR A  83 "
            model="   0" pdb=" CB  THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.49e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.068 2.00e-02 2.50e+03   2.70e-02 2.19e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.063 2.00e-02 2.50e+03   2.69e-02 2.16e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.039 2.00e-02 2.50e+03   1.83e-02 1.01e+01
        model="   0" pdb=" CG  TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 159
        2.21 -     2.80: 4402
        2.80 -     3.40: 5995
        3.40 -     4.00: 7203
        4.00 -     4.60: 10881
  Nonbonded interactions: 28640
  Sorted by model distance:
  nonbonded model="   0" pdb=" HA  ILE A  86 "
            model="   0" pdb=" HE2 TYR A  89 "
     model   vdw
     1.607 2.270
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.693 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.731 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.761 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.782 1.850
  ... (remaining 28635 not shown)

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

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


  Symmetric amino acids flipped
    Residue "A TYR   89": "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: "   0"
    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: 2224
  At special positions: 0
  Unit cell: (50.314, 44.193, 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    1113      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)----------                  

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: {'PTRANS': 7, 'TRANS': 131}

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

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

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

  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (69.3, 48.026, 48.024, 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      : 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:    0.038 (Z=  2.752)
  Mean delta:    0.011 (Z=  0.579)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   129.21    -7.51  1.80e+00  1.74e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.512 (Z=  4.174)
  Mean delta:    1.590 (Z=  0.874)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  48  ALA  CA
   A  48  ALA  C
   A  49  GLU  N
   A  49  GLU  CA        180.00   149.17    30.83  5.00e+00  3.80e+01   6.2*sigma

  Min. delta:    0.007
  Max. delta:   89.399
  Mean delta:   12.025

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:    0.254
  Mean delta:    0.078

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.412
    Angle     :  1.531   7.512   4079  Z= 0.665
    Chirality :  0.078   0.254    176
    Planarity :  0.008   0.037    327
    Dihedral  : 10.321  89.399    769
    Min Nonbonded Distance : 1.701
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.19 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  1.61 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    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: -0.21 (0.68), residues: 137
    helix:  0.45 (0.52), residues: 82
    sheet: -3.50 (0.99), residues: 12
    loop :  0.06 (1.01), residues: 43
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.020   0.004   PHE A  45 
   TYR   0.054   0.008   TYR A 111 
   ARG   0.038   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.013   0.004   PHE A  45 
   TYR   0.044   0.009   TYR A 111 
   ARG   0.005   0.002   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   1.46 %
                favored =  96.35 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0079
  RMS(angles)           =   1.53
  MolProbity score      =   1.88

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:    0.040 (Z=  2.713)
  Mean delta:    0.012 (Z=  0.605)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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:    0.001 (Z=  0.001)
  Max. delta:    7.335 (Z=  4.104)
  Mean delta:    1.604 (Z=  0.882)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.021
  Max. delta:   86.730
  Mean delta:   12.683

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.228
  Mean delta:    0.079

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.076
  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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.431
    Angle     :  1.544   7.335   4079  Z= 0.671
    Chirality :  0.079   0.228    176
    Planarity :  0.009   0.060    327
    Dihedral  : 12.030  86.730    769
    Min Nonbonded Distance : 1.184
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  2.42 %
      Favored  : 95.16 %
    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:  0.51 (0.71), residues: 137
    helix: -0.02 (0.48), residues: 90
    sheet: -1.72 (1.64), residues: 10
    loop :  2.60 (1.18), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.140   0.017   TYR A  81 
   ARG   0.061   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.011   0.002   PHE A  67 
   TYR   0.114   0.020   TYR A  81 
   ARG   0.008   0.002   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=  2.900)
  Mean delta:    0.012 (Z=  0.624)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.52     4.08  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.413 (Z=  4.082)
  Mean delta:    1.596 (Z=  0.872)

                      ----------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   156.59    23.41  5.00e+00  2.19e+01   4.7*sigma

  Min. delta:    0.025
  Max. delta:   87.053
  Mean delta:   12.742

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.206
  Mean delta:    0.078

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.050
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.037   2242  Z= 0.444
    Angle     :  1.539   6.413   4079  Z= 0.666
    Chirality :  0.078   0.206    176
    Planarity :  0.008   0.041    327
    Dihedral  : 11.757  87.389    769
    Min Nonbonded Distance : 1.626
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  4.03 %
      Favored  : 92.74 %
    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:  0.04 (0.69), residues: 137
    helix:  0.02 (0.48), residues: 94
    sheet: -1.85 (1.48), residues: 10
    loop :  1.35 (1.26), residues: 33
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.012   0.003   PHE A  45 
   TYR   0.089   0.015   TYR A  81 
   ARG   0.042   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.011   0.003   PHE A  67 
   TYR   0.074   0.018   TYR A  81 
   ARG   0.005   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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


============================== 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)----------                  

  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.54
  MolProbity score      =   1.80

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.54
  MolProbity score      =   1.90

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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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 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  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: "   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: 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.


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:    0.044 (Z=  3.397)
  Mean delta:    0.012 (Z=  0.615)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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:    0.001 (Z=  0.001)
  Max. delta:    7.614 (Z=  4.059)
  Mean delta:    1.617 (Z=  0.864)

                      ----------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   150.16    29.84  5.00e+00  3.56e+01   6.0*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   154.18    25.82  5.00e+00  2.67e+01   5.2*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   156.12    23.88  5.00e+00  2.28e+01   4.8*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   158.28    21.72  5.00e+00  1.89e+01   4.3*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   158.60    21.40  5.00e+00  1.83e+01   4.3*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   159.52    20.48  5.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.014
  Max. delta:   75.890
  Mean delta:   11.441

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.188
  Mean delta:    0.073

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.046
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.044   2242  Z= 0.438
    Angle     :  1.542   7.614   4079  Z= 0.661
    Chirality :  0.073   0.188    176
    Planarity :  0.008   0.046    327
    Dihedral  : 10.264  75.890    769
    Min Nonbonded Distance : 1.675
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  4.38 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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: -0.72 (0.71), residues: 137
    helix: -0.32 (0.55), residues: 74
    sheet:  None (None), residues: 0
    loop : -0.51 (0.87), residues: 63
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.019   0.004   PHE A  45 
   TYR   0.060   0.009   TYR A  50 
   ARG   0.040   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  45 
   TYR   0.050   0.011   TYR A  50 
   ARG   0.004   0.001   ARG A 127 

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

   A 100  GLN
   A  66  GLN

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

  Histogram of bond lengths:
        0.84 -     1.03: 1113
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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="   0" pdb=" CZ  ARG A  21 "
       model="   0" 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="   0" pdb=" CZ  ARG A 127 "
       model="   0" 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="   0" pdb=" CD  ARG A  21 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       27.80 -    48.41: 1
       48.41 -    69.03: 0
       69.03 -    89.64: 0
       89.64 -   110.26: 2238
      110.26 -   130.87: 1852
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   27.80   81.67 3.00e+00 1.11e-01 7.41e+02
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  122.73  -13.26 3.00e+00 1.11e-01 1.95e+01
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.17   -9.70 3.00e+00 1.11e-01 1.04e+01
  angle model="   0" pdb=" CA  GLY A  94 "
        model="   0" pdb=" N   GLY A  94 "
        model="   0" pdb=" H   GLY A  94 "
      ideal   model   delta    sigma   weight residual
     114.00  119.91   -5.91 3.00e+00 1.11e-01 3.88e+00
  angle model="   0" pdb=" CA  GLY A  73 "
        model="   0" pdb=" N   GLY A  73 "
        model="   0" pdb=" H   GLY A  73 "
      ideal   model   delta    sigma   weight residual
     114.00  119.88   -5.88 3.00e+00 1.11e-01 3.85e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 809
       16.92 -    33.84: 104
       33.84 -    50.76: 73
       50.76 -    67.68: 44
       67.68 -    84.60: 9
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A  88 "
           model="   0" pdb=" CB  ASP A  88 "
           model="   0" pdb=" CG  ASP A  88 "
           model="   0" 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="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" CB  ASP A 118 "
           model="   0" pdb=" CG  ASP A 118 "
           model="   0" 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="   0" pdb=" CB  GLU A 120 "
           model="   0" pdb=" CG  GLU A 120 "
           model="   0" pdb=" CD  GLU A 120 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" 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="   0" pdb=" CA  ILE A  38 "
            model="   0" pdb=" N   ILE A  38 "
            model="   0" pdb=" C   ILE A  38 "
            model="   0" 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="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" 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="   0" pdb=" CB  TYR A 111 "   -0.001 2.00e-02 2.50e+03   6.89e-04 1.42e-02
        model="   0" pdb=" CG  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.000 2.00e-02 2.50e+03   6.08e-04 1.11e-02
        model="   0" pdb=" CG  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "    0.000 2.00e-02 2.50e+03   5.86e-04 1.03e-02
        model="   0" pdb=" CG  TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "    0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.45: 1296
        2.45 -     2.99: 5101
        2.99 -     3.52: 5549
        3.52 -     4.06: 6905
        4.06 -     4.60: 9754
  Nonbonded interactions: 28605
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ILE A 108 "
            model="   0" pdb=" H   TYR A 111 "
     model   vdw
     1.910 1.850
  nonbonded model="   0" pdb=" O   THR A  56 "
            model="   0" pdb=" H   ALA A  60 "
     model   vdw
     1.911 1.850
  nonbonded model="   0" pdb=" O   LEU A   9 "
            model="   0" pdb=" H   SER A  13 "
     model   vdw
     1.912 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.923 1.850
  nonbonded model="   0" pdb=" O   LEU A 132 "
            model="   0" pdb=" H   HIS A 134 "
     model   vdw
     1.934 1.850
  ... (remaining 28600 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)----------                  

  Ramachandran outliers =   3.65 %
                favored =  91.97 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.54
  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)----------                  


============================== 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 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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      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:    0.038 (Z=  2.970)
  Mean delta:    0.012 (Z=  0.621)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   130.56    -8.86  1.80e+00  2.42e+01   4.9*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:    0.000 (Z=  0.000)
  Max. delta:    8.857 (Z=  4.920)
  Mean delta:    1.661 (Z=  0.914)

                      ----------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   151.33    28.67  5.00e+00  3.29e+01   5.7*sigma

  Min. delta:    0.003
  Max. delta:   86.210
  Mean delta:   12.285

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.205
  Mean delta:    0.078

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.049
  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----------                   

    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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.442
    Angle     :  1.577   8.857   4079  Z= 0.690
    Chirality :  0.078   0.205    176
    Planarity :  0.008   0.037    327
    Dihedral  : 10.944  86.210    769
    Min Nonbonded Distance : 1.488
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  2.19 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  2.42 %
      Favored  : 96.77 %
    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: -0.45 (0.69), residues: 137
    helix: -0.35 (0.48), residues: 91
    sheet: -1.97 (1.65), residues: 10
    loop :  1.02 (1.17), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.013   0.003   PHE A  45 
   TYR   0.081   0.012   TYR A 111 
   ARG   0.040   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.010   0.003   PHE A  67 
   TYR   0.067   0.015   TYR A 111 
   ARG   0.004   0.001   ARG A 127 

                     ----------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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   2.19 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.58
  MolProbity score      =   1.46

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: 0.98
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 seconds

  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:    0.025 (Z=  1.362)
  Mean delta:    0.004 (Z=  0.238)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.515 (Z=  1.553)
  Mean delta:    0.637 (Z=  0.319)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   73.504
  Mean delta:    9.705

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.137
  Mean delta:    0.036

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.019
  Mean delta:    0.003

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.025   2242  Z= 0.170
    Angle     :  1.042   4.911   4079  Z= 0.377
    Chirality :  0.036   0.137    176
    Planarity :  0.002   0.019    327
    Dihedral  :  9.698  73.504    769
    Min Nonbonded Distance : 1.571
  
  Molprobity Statistics.
    All-atom Clashscore : 14.43
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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: -0.91 (0.69), residues: 137
    helix: -0.54 (0.54), residues: 70
    sheet: -0.26 (1.53), residues: 10
    loop : -0.53 (0.90), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.006   0.002   PHE A  45 
   TYR   0.008   0.002   TYR A  81 
   ARG   0.008   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.007   0.001   TYR A 111 
   ARG   0.002   0.001   ARG A  21 

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

   A 137  HIS
   A 134  HIS

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 3
        1.22 -     1.42: 457
        1.42 -     1.61: 672
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   GLU A 123 "
       model="   0" pdb=" N   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.93e+00
  bond model="   0" pdb=" C   GLU A 133 "
       model="   0" pdb=" N   HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.69e+00
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.38e+00
  bond model="   0" pdb=" C   LYS A  40 "
       model="   0" pdb=" N   VAL A  41 "
    ideal  model  delta    sigma   weight residual
    1.329  1.342 -0.013 1.40e-02 5.10e+03 9.25e-01
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.331 -0.010 1.00e-02 1.00e+04 9.06e-01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.68 -   106.75: 54
      106.75 -   112.82: 2721
      112.82 -   118.89: 435
      118.89 -   124.96: 827
      124.96 -   131.03: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" C   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     112.10  106.57    5.53 2.50e+00 1.60e-01 4.89e+00
  angle model="   0" pdb=" N   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     110.00  115.19   -5.19 3.00e+00 1.11e-01 3.00e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  123.14   -5.14 3.00e+00 1.11e-01 2.93e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.60   -4.60 3.00e+00 1.11e-01 2.35e+00
  angle model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" CB  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     111.60  108.61    2.99 2.00e+00 2.50e-01 2.23e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 988
       17.65 -    35.29: 20
       35.29 -    52.94: 10
       52.94 -    70.59: 5
       70.59 -    88.23: 10
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.23   88.23     1      3.00e+01 1.11e-03 1.03e+01
  dihedral model="   0" pdb=" CB  GLU A 123 "
           model="   0" pdb=" CG  GLU A 123 "
           model="   0" pdb=" CD  GLU A 123 "
           model="   0" pdb=" OE1 GLU A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.64  -85.64     1      3.00e+01 1.11e-03 9.86e+00
  dihedral model="   0" pdb=" CB  GLU A  75 "
           model="   0" pdb=" CG  GLU A  75 "
           model="   0" pdb=" CD  GLU A  75 "
           model="   0" pdb=" OE1 GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -81.75   81.75     1      3.00e+01 1.11e-03 9.14e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 112
       0.028 -    0.057: 44
       0.057 -    0.085: 6
       0.085 -    0.113: 11
       0.113 -    0.141: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.98e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality model="   0" pdb=" CA  HIS A 134 "
            model="   0" pdb=" N   HIS A 134 "
            model="   0" pdb=" C   HIS A 134 "
            model="   0" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.25e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 134 "   -0.009 2.00e-02 2.50e+03   7.00e-03 9.79e-01
        model="   0" pdb=" CG  HIS A 134 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 134 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 134 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 134 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 134 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 134 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 134 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  PRO A  52 "    0.004 2.00e-02 2.50e+03   8.09e-03 6.54e-01
        model="   0" pdb=" C   PRO A  52 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" O   PRO A  52 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" N   LEU A  53 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 135 "   -0.007 2.00e-02 2.50e+03   5.51e-03 6.08e-01
        model="   0" pdb=" CG  HIS A 135 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 135 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 135 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 135 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 135 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 135 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 135 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 89
        2.12 -     2.74: 4054
        2.74 -     3.36: 5866
        3.36 -     3.98: 7322
        3.98 -     4.60: 11200
  Nonbonded interactions: 28531
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.497 1.850
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.630 1.850
  nonbonded model="   0" pdb=" H   ILE A  78 "
            model="   0" pdb=" O   THR A  92 "
     model   vdw
     1.717 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb=" O   ILE A  78 "
            model="   0" pdb=" H   THR A  92 "
     model   vdw
     1.740 1.850
  ... (remaining 28526 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: (74.027, 46.566, 57.795, 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: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.31, 75.355, 51.064, 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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  14.43
  RMS(bonds)            =   0.0029
  RMS(angles)           =   1.04
  MolProbity score      =   1.97

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 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: "   0"
    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      : 2224
     H or D atoms   : 1113
     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 : 1113
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1113
  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 
    0" pdbres="HIS A 134  conformer  : HE2 
    0" pdbres="HIS A 135  conformer  : HE2 
    0" pdbres="HIS A 136  conformer  : HE2 
    0" pdbres="HIS A 137  conformer  : HE2 
    0" pdbres="HIS A 138  conformer  : HE2 
    0" pdbres="HIS A 139  conformer  : HE2 

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

   A   1  MET  H2 , Angle H1-N-H2, observed: 131.317, delta from target: -21.847
   A   1  MET  H3 , Angle H1-N-H3, observed: 56.250, delta from target: 53.220

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2248  Z= 0.045
    Angle     :  1.701  53.220   4091  Z= 0.576
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 23.183  80.483    775
    Min Nonbonded Distance : 1.906
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    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   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   TYR A  12 
   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 ===================================


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

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)----------                  

        Number of residues, atoms: 139, 2224
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

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

  Ramachandran outliers =   2.92 %
                favored =  78.83 %
  Rotamer outliers      =  26.61 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0009
  RMS(angles)           =   1.70
  MolProbity score      =   2.33

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:    0.041 (Z=  2.758)
  Mean delta:    0.011 (Z=  0.600)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.891 (Z=  3.816)
  Mean delta:    1.606 (Z=  0.874)

                      ----------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   155.85    24.15  5.00e+00  2.33e+01   4.8*sigma

  Min. delta:    0.041
  Max. delta:   85.868
  Mean delta:   12.119

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.259
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.054
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.041   2242  Z= 0.427
    Angle     :  1.537   6.891   4079  Z= 0.665
    Chirality :  0.076   0.259    176
    Planarity :  0.008   0.040    327
    Dihedral  : 11.301  85.868    769
    Min Nonbonded Distance : 1.467
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  3.23 %
      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:  0.62 (0.70), residues: 137
    helix:  0.88 (0.53), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.14 (0.91), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.015   0.004   PHE A  67 
   TYR   0.065   0.010   TYR A 111 
   ARG   0.045   0.009   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.008   0.003   PHE A  67 
   TYR   0.055   0.012   TYR A 111 
   ARG   0.005   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


  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   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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.99, per 1000 atoms: 0.45
  Number of scatterers: 2224
  At special positions: 0
  Unit cell: (68.994, 46.48, 57.764, 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    1113      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.54
  MolProbity score      =   1.86

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=  2.736)
  Mean delta:    0.011 (Z=  0.586)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.228 (Z=  3.762)
  Mean delta:    1.546 (Z=  0.855)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -157.15   -22.85  5.00e+00  2.09e+01   4.6*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00  -158.62   -21.38  5.00e+00  1.83e+01   4.3*sigma

  Min. delta:    0.006
  Max. delta:   86.065
  Mean delta:   11.694

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.231
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.049
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.417
    Angle     :  1.508   6.228   4079  Z= 0.654
    Chirality :  0.076   0.231    176
    Planarity :  0.008   0.038    327
    Dihedral  : 10.427  86.065    769
    Min Nonbonded Distance : 1.493
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.81 %
      Favored  : 97.58 %
    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: -0.12 (0.70), residues: 137
    helix:  0.10 (0.52), residues: 87
    sheet: -2.30 (1.00), residues: 12
    loop :  0.77 (1.16), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A  43 
   PHE   0.019   0.004   PHE A  67 
   TYR   0.076   0.010   TYR A 111 
   ARG   0.040   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A  43 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.062   0.012   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

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

   A  43  HIS
   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=  0.000)
  Max. delta:    0.057 (Z=  3.089)
  Mean delta:    0.012 (Z=  0.619)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.834 (Z=  3.868)
  Mean delta:    1.569 (Z=  0.863)

                      ----------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   157.14    22.86  5.00e+00  2.09e+01   4.6*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   157.72    22.28  5.00e+00  1.99e+01   4.5*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   158.81    21.19  5.00e+00  1.80e+01   4.2*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   159.65    20.35  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.010
  Max. delta:   84.622
  Mean delta:   11.190

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.204
  Mean delta:    0.072

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.057   2242  Z= 0.441
    Angle     :  1.511   6.834   4079  Z= 0.657
    Chirality :  0.072   0.204    176
    Planarity :  0.007   0.042    327
    Dihedral  : 10.422  84.622    769
    Min Nonbonded Distance : 1.609
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.11 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.81 %
      Favored  : 98.39 %
    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:  0.07 (0.70), residues: 137
    helix: -0.10 (0.60), residues: 63
    sheet: -1.13 (1.11), residues: 10
    loop :  0.67 (0.84), residues: 64
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 136 
   PHE   0.013   0.003   PHE A  45 
   TYR   0.078   0.010   TYR A  50 
   ARG   0.040   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 136 
   PHE   0.010   0.003   PHE A  67 
   TYR   0.065   0.012   TYR A  50 
   ARG   0.005   0.001   ARG A  21 

                     ----------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 =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0081
  RMS(angles)           =   1.51
  MolProbity score      =   1.57

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 =   2.19 %
                favored =  92.70 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   7.66
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.51
  MolProbity score      =   1.88

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

  Symmetric amino acids flipped
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "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: "   0"
    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}
        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 ==============================

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

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


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

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.201, 50.985, 78.602, 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: (55.49, 49.154, 44.329, 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 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 ==============================


============================== 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:    0.038 (Z=  2.893)
  Mean delta:    0.012 (Z=  0.622)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   130.78    -9.08  1.80e+00  2.54e+01   5.0*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:    0.002 (Z=  0.001)
  Max. delta:    9.076 (Z=  5.042)
  Mean delta:    1.629 (Z=  0.890)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -155.65   -24.35  5.00e+00  2.37e+01   4.9*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00  -156.55   -23.45  5.00e+00  2.20e+01   4.7*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   159.21    20.79  5.00e+00  1.73e+01   4.2*sigma

  Min. delta:    0.029
  Max. delta:   82.100
  Mean delta:   12.530

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.249
  Mean delta:    0.078

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.055
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.443
    Angle     :  1.571   9.076   4079  Z= 0.680
    Chirality :  0.078   0.249    176
    Planarity :  0.007   0.042    327
    Dihedral  : 11.291  82.100    769
    Min Nonbonded Distance : 1.734
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  2.42 %
      Favored  : 95.97 %
    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:  0.68 (0.66), residues: 137
    helix:  0.18 (0.53), residues: 76
    sheet:  None (None), residues: 0
    loop :  1.12 (0.77), residues: 61
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.070   0.010   TYR A  50 
   ARG   0.045   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.012   0.004   PHE A  67 
   TYR   0.057   0.012   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

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

   A  66  GLN

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


  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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.57
  MolProbity score      =   1.42

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 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: "   0"
    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: (51.34, 63.356, 69.8, 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: (44.668, 44.046, 52.748, 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 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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      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}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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 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: "   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: 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: 1.02
  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.

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 -     1.24: 135
        1.24 -     1.43: 337
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.15e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.35e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 5.08e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 5.01e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.89e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.07 -   106.96: 190
      106.96 -   112.84: 2556
      112.84 -   118.73: 431
      118.73 -   124.62: 829
      124.62 -   130.51: 73
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  130.51   -8.81 1.80e+00 3.09e-01 2.40e+01
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  130.11   -8.41 1.80e+00 3.09e-01 2.18e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.50    4.10 1.00e+00 1.00e+00 1.68e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.56   -3.96 1.00e+00 1.00e+00 1.56e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.30   -3.70 1.00e+00 1.00e+00 1.37e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 974
       17.43 -    34.86: 44
       34.86 -    52.29: 10
       52.29 -    69.72: 3
       69.72 -    87.15: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  VAL A 112 "
           model="   0" pdb=" C   VAL A 112 "
           model="   0" pdb=" N   LYS A 113 "
           model="   0" pdb=" CA  LYS A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.15   17.85     0      5.00e+00 4.00e-02 1.27e+01
  dihedral model="   0" pdb=" N   ARG A 127 "
           model="   0" pdb=" CA  ARG A 127 "
           model="   0" pdb=" CB  ARG A 127 "
           model="   0" pdb=" CG  ARG A 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.90  -56.10     3      1.50e+01 4.44e-03 9.38e+00
  dihedral model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" C   ASP A 116 "
           model="   0" pdb=" N   PRO A 117 "
           model="   0" pdb=" CA  PRO A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.26  -14.74     0      5.00e+00 4.00e-02 8.69e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 76
       0.046 -    0.092: 56
       0.092 -    0.138: 28
       0.138 -    0.184: 13
       0.184 -    0.229: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" 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 1.32e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality model="   0" pdb=" CA  THR A  83 "
            model="   0" pdb=" N   THR A  83 "
            model="   0" pdb=" C   THR A  83 "
            model="   0" pdb=" CB  THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.154 2.00e-02 2.50e+03   6.61e-02 1.31e+02
        model="   0" pdb=" CG  TYR A  81 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.127 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.036 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.098 2.00e-02 2.50e+03   3.74e-02 4.19e+01
        model="   0" pdb=" CG  TYR A  91 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.079 2.00e-02 2.50e+03   3.20e-02 3.07e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.009 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.17: 128
        2.17 -     2.78: 4162
        2.78 -     3.39: 6068
        3.39 -     3.99: 7186
        3.99 -     4.60: 10990
  Nonbonded interactions: 28534
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ  PHE A  67 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.565 2.100
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.607 1.850
  nonbonded model="   0" pdb=" HH  TYR A  81 "
            model="   0" pdb=" HH  TYR A  91 "
     model   vdw
     1.724 2.100
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.739 1.850
  nonbonded model="   0" pdb=" O   ILE A 122 "
            model="   0" pdb=" H   VAL A 126 "
     model   vdw
     1.739 1.850
  ... (remaining 28529 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 -     1.04: 1106
        1.04 -     1.23: 93
        1.23 -     1.43: 379
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.78e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.62e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.38e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.37e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.20 -   105.95: 80
      105.95 -   111.69: 2471
      111.69 -   117.44: 506
      117.44 -   123.18: 815
      123.18 -   128.93: 207
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" CB  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     103.00  107.29   -4.29 1.10e+00 8.26e-01 1.52e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.55    4.65 1.30e+00 5.92e-01 1.28e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.59    4.61 1.30e+00 5.92e-01 1.26e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.20    3.40 1.00e+00 1.00e+00 1.16e+01
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  127.75   -6.05 1.80e+00 3.09e-01 1.13e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 967
       17.26 -    34.51: 40
       34.51 -    51.77: 19
       51.77 -    69.02: 5
       69.02 -    86.28: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.70  -19.30     0      5.00e+00 4.00e-02 1.49e+01
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.19   15.81     0      5.00e+00 4.00e-02 1.00e+01
  dihedral model="   0" pdb=" N   HIS A 135 "
           model="   0" pdb=" CA  HIS A 135 "
           model="   0" pdb=" CB  HIS A 135 "
           model="   0" pdb=" CG  HIS A 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.55   58.55     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 77
       0.042 -    0.084: 51
       0.084 -    0.125: 30
       0.125 -    0.167: 15
       0.167 -    0.209: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.89e-01
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.34e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.084 2.00e-02 2.50e+03   3.69e-02 4.10e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.075 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.022 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.066 2.00e-02 2.50e+03   2.59e-02 2.01e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.062 2.00e-02 2.50e+03   2.41e-02 1.74e+01
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.015 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.005 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 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 203
        2.22 -     2.81: 4533
        2.81 -     3.41: 6019
        3.41 -     4.00: 7363
        4.00 -     4.60: 11102
  Nonbonded interactions: 29220
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.621 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.726 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.766 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.780 1.850
  ... (remaining 29215 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      : 2224
     H or D atoms   : 1113
     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 : 1113
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1113
  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 
    0" pdbres="HIS A 134  conformer  : HE2 
    0" pdbres="HIS A 135  conformer  : HE2 
    0" pdbres="HIS A 136  conformer  : HE2 
    0" pdbres="HIS A 137  conformer  : HE2 
    0" pdbres="HIS A 138  conformer  : HE2 
    0" pdbres="HIS A 139  conformer  : HE2 

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

   A   1  MET  H2 , Angle H1-N-H2, observed: 75.081, delta from target: 34.389
   A   1  MET  H3 , Angle H1-N-H3, observed: 34.609, delta from target: 74.861

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2248  Z= 0.046
    Angle     :  1.935  74.861   4091  Z= 0.653
    Chirality :  0.035   0.096    176
    Planarity :  0.000   0.001    326
    Dihedral  : 23.234  89.565    775
    Min Nonbonded Distance : 1.917
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    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   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   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----------                     

  No backwards Asn/Gln/His sidechains found.

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

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (61.387, 84.012, 35.49, 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)----------                  


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=  2.584)
  Mean delta:    0.012 (Z=  0.622)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.652 (Z=  3.590)
  Mean delta:    1.702 (Z=  0.898)

                      ----------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   147.87    32.13  5.00e+00  4.13e+01   6.4*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   149.23    30.77  5.00e+00  3.79e+01   6.2*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   150.72    29.28  5.00e+00  3.43e+01   5.9*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   156.95    23.05  5.00e+00  2.13e+01   4.6*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   157.33    22.67  5.00e+00  2.06e+01   4.5*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   158.09    21.91  5.00e+00  1.92e+01   4.4*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   158.38    21.62  5.00e+00  1.87e+01   4.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   158.70    21.30  5.00e+00  1.81e+01   4.3*sigma

  Min. delta:    0.033
  Max. delta:   84.650
  Mean delta:   12.308

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.227
  Mean delta:    0.078

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.049
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.443
    Angle     :  1.600   7.652   4079  Z= 0.684
    Chirality :  0.078   0.227    176
    Planarity :  0.008   0.037    327
    Dihedral  : 11.306  84.650    769
    Min Nonbonded Distance : 1.534
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers : 10.22 %
      Allowed  :  5.84 %
      Favored  : 83.94 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  2.42 %
      Favored  : 96.77 %
    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: -1.75 (0.70), residues: 137
    helix: -0.67 (0.54), residues: 69
    sheet:  None (None), residues: 0
    loop : -1.64 (0.83), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.011   0.003   PHE A  67 
   TYR   0.071   0.011   TYR A  50 
   ARG   0.042   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.010   0.003   PHE A  67 
   TYR   0.059   0.013   TYR A  50 
   ARG   0.005   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: {'PTRANS': 7, 'TRANS': 131}
  Ramachandran outliers =   5.84 %
                favored =  75.91 %
  Rotamer outliers      =  22.58 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0009
  RMS(angles)           =   1.94
  MolProbity score      =   2.31

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.73, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.864, 44.225, 55.527, 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}
  Ramachandran outliers =  10.22 %
                favored =  83.94 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.60
  MolProbity score      =   1.83

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: 1.10
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.23 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 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   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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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 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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1113
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" NE  ARG A  21 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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="   0" pdb=" CZ  ARG A  21 "
       model="   0" 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="   0" pdb=" CZ  ARG A  58 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       57.81 -    72.49: 1
       72.49 -    87.18: 0
       87.18 -   101.86: 2
      101.86 -   116.55: 3008
      116.55 -   131.23: 1080
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   57.81   51.66 3.00e+00 1.11e-01 2.97e+02
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  131.23  -21.76 3.00e+00 1.11e-01 5.26e+01
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.16   -9.69 3.00e+00 1.11e-01 1.04e+01
  angle model="   0" pdb=" CA  GLY A  96 "
        model="   0" pdb=" N   GLY A  96 "
        model="   0" pdb=" H   GLY A  96 "
      ideal   model   delta    sigma   weight residual
     114.00  119.89   -5.89 3.00e+00 1.11e-01 3.85e+00
  angle model="   0" pdb=" CA  GLY A  73 "
        model="   0" pdb=" N   GLY A  73 "
        model="   0" pdb=" H   GLY A  73 "
      ideal   model   delta    sigma   weight residual
     114.00  119.87   -5.87 3.00e+00 1.11e-01 3.83e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 801
       17.63 -    35.26: 129
       35.26 -    52.89: 66
       52.89 -    70.52: 37
       70.52 -    88.15: 6
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  85 "
           model="   0" pdb=" CB  LYS A  85 "
           model="   0" pdb=" CG  LYS A  85 "
           model="   0" 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="   0" pdb=" CA  MET A   1 "
           model="   0" pdb=" CB  MET A   1 "
           model="   0" pdb=" CG  MET A   1 "
           model="   0" 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="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" CB  ASP A 116 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A 108 "
            model="   0" pdb=" N   ILE A 108 "
            model="   0" pdb=" C   ILE A 108 "
            model="   0" 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="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" 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="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" 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="   0" pdb=" CB  TYR A  68 "    0.001 2.00e-02 2.50e+03   5.79e-04 1.01e-02
        model="   0" pdb=" CG  TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.001 2.00e-02 2.50e+03   5.67e-04 9.64e-03
        model="   0" pdb=" CG  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.001 2.00e-02 2.50e+03   4.99e-04 7.48e-03
        model="   0" pdb=" CG  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.000 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.44: 1261
        2.44 -     2.98: 5266
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:    0.025 (Z=  1.778)
  Mean delta:    0.004 (Z=  0.228)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.029 (Z=  1.423)
  Mean delta:    0.820 (Z=  0.395)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   88.186
  Mean delta:   10.881

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.145
  Mean delta:    0.038

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.023
  Mean delta:    0.003

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.025   2242  Z= 0.163
    Angle     :  1.113   5.348   4079  Z= 0.410
    Chirality :  0.038   0.145    176
    Planarity :  0.003   0.023    327
    Dihedral  : 10.125  88.186    769
    Min Nonbonded Distance : 1.247
  
  Molprobity Statistics.
    All-atom Clashscore : 10.37
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.73 %
      Favored  : 99.27 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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:  0.92 (0.71), residues: 137
    helix:  0.71 (0.61), residues: 63
    sheet:  None (None), residues: 0
    loop :  0.71 (0.77), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.008   0.002   PHE A  67 
   TYR   0.014   0.003   TYR A 111 
   ARG   0.005   0.001   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.007   0.002   PHE A  67 
   TYR   0.014   0.003   TYR A 111 
   ARG   0.001   0.000   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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


        2.98 -     3.52: 5512
        3.52 -     4.06: 6997
        4.06 -     4.60: 10012
  Nonbonded interactions: 29048
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LEU A   9 "
            model="   0" pdb=" H   SER A  13 "
     model   vdw
     1.906 1.850
  nonbonded model="   0" pdb=" O   PRO A 117 "
            model="   0" pdb=" H   LEU A 119 "
     model   vdw
     1.912 1.850
  nonbonded model="   0" pdb=" O   LYS A 125 "
            model="   0" pdb=" H   ARG A 129 "
     model   vdw
     1.922 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.949 1.850
  nonbonded model="   0" pdb=" O   TYR A  68 "
            model="   0" pdb="HD21 ASN A  72 "
     model   vdw
     1.954 1.850
  ... (remaining 29043 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2224
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 0.69, per 1000 atoms: 0.31
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (58.632, 45.154, 61.817, 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: 1.04, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.333, 47.071, 48.778, 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      : 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:    0.038 (Z=  2.804)
  Mean delta:    0.012 (Z=  0.606)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.148 (Z=  4.228)
  Mean delta:    1.586 (Z=  0.867)

                      ----------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   151.07    28.93  5.00e+00  3.35e+01   5.8*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   157.35    22.65  5.00e+00  2.05e+01   4.5*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   158.19    21.81  5.00e+00  1.90e+01   4.4*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   159.86    20.14  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.034
  Max. delta:   89.773
  Mean delta:   13.124

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.205
  Mean delta:    0.075

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.043
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.432
    Angle     :  1.524   6.148   4079  Z= 0.661
    Chirality :  0.075   0.205    176
    Planarity :  0.007   0.033    327
    Dihedral  : 11.208  89.773    769
    Min Nonbonded Distance : 1.666
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  4.38 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  3.23 %
      Favored  : 93.55 %
    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: -0.51 (0.69), residues: 137
    helix: -0.09 (0.48), residues: 92
    sheet:  None (None), residues: 0
    loop : -0.59 (1.06), residues: 45
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.012   0.003   PHE A  45 
   TYR   0.061   0.009   TYR A 111 
   ARG   0.037   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.051   0.011   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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


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

  Ramachandran outliers =   0.00 %
                favored =  99.27 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  10.37
  RMS(bonds)            =   0.0027
  RMS(angles)           =   1.11
  MolProbity score      =   1.54

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 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: "   0"
    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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   2.19 %
                favored =  93.43 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.52
  MolProbity score      =   2.11

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

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

  Time building chain proxies: 1.25, per 1000 atoms: 0.56
  Number of scatterers: 2224
  At special positions: 0
  Unit cell: (51.185, 56.683, 58.107, 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    1113      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: (64.546, 63.795, 41.508, 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: 1.13 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: 1.02
  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.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     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="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.19e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.14e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.46e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.40e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.37e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.09 -   106.69: 154
      106.69 -   112.29: 2521
      112.29 -   117.89: 414
      117.89 -   123.49: 836
      123.49 -   129.09: 154
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.40    4.20 1.00e+00 1.00e+00 1.76e+01
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  129.09   -7.39 1.80e+00 3.09e-01 1.68e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.60    4.60 1.30e+00 5.92e-01 1.25e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.13    3.47 1.00e+00 1.00e+00 1.20e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.88   -3.28 1.00e+00 1.00e+00 1.08e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 971
       17.05 -    34.09: 43
       34.09 -    51.14: 15
       51.14 -    68.18: 2
       68.18 -    85.23: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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  160.78   19.22     0      5.00e+00 4.00e-02 1.48e+01
  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  164.51   15.49     0      5.00e+00 4.00e-02 9.60e+00
  dihedral model="   0" pdb=" CA  VAL A 112 "
           model="   0" pdb=" C   VAL A 112 "
           model="   0" pdb=" N   LYS A 113 "
           model="   0" pdb=" CA  LYS A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.53   15.47     0      5.00e+00 4.00e-02 9.58e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 79
       0.040 -    0.080: 43
       0.080 -    0.120: 29
       0.120 -    0.160: 24
       0.160 -    0.200: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.00e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.34e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.61e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.063 2.00e-02 2.50e+03   2.81e-02 2.37e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 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 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.056 2.00e-02 2.50e+03   2.18e-02 1.42e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.041 2.00e-02 2.50e+03   1.54e-02 7.09e+00
        model="   0" pdb=" CG  TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 239
        2.25 -     2.84: 4739
        2.84 -     3.43: 5706
        3.43 -     4.01: 7231
        4.01 -     4.60: 10729
  Nonbonded interactions: 28644
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.663 1.850
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.719 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.741 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.743 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.779 1.850
  ... (remaining 28639 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 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: "   0"
    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 -     1.04: 1106
        1.04 -     1.23: 116
        1.23 -     1.43: 356
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.353 -0.032 1.00e-02 1.00e+04 1.00e+01
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 8.89e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.32e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" 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="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    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:
      100.39 -   106.06: 100
      106.06 -   111.74: 2466
      111.74 -   117.41: 499
      117.41 -   123.08: 790
      123.08 -   128.76: 224
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  117.14   -4.54 1.00e+00 1.00e+00 2.06e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.48    4.12 1.00e+00 1.00e+00 1.70e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.54   -3.94 1.00e+00 1.00e+00 1.55e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.22    4.98 1.30e+00 5.92e-01 1.47e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.12    3.48 1.00e+00 1.00e+00 1.21e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 970
       16.65 -    33.30: 47
       33.30 -    49.95: 12
       49.95 -    66.60: 2
       66.60 -    83.25: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.20   27.80     0      5.00e+00 4.00e-02 3.09e+01
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.40   25.60     0      5.00e+00 4.00e-02 2.62e+01
  dihedral model="   0" pdb=" CA  HIS A 134 "
           model="   0" pdb=" C   HIS A 134 "
           model="   0" pdb=" N   HIS A 135 "
           model="   0" pdb=" CA  HIS A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.00   25.00     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 84
       0.047 -    0.094: 52
       0.094 -    0.140: 31
       0.140 -    0.187: 7
       0.187 -    0.233: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.80e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.73e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.063 2.00e-02 2.50e+03   2.71e-02 2.21e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.012 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 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.061 2.00e-02 2.50e+03   2.46e-02 1.82e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.019 2.00e-02 2.50e+03   3.93e-02 1.55e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.068 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.16: 114
        2.16 -     2.77: 4130
        2.77 -     3.38: 6072
        3.38 -     3.99: 7235
        3.99 -     4.60: 10955
  Nonbonded interactions: 28506
  Sorted by model distance:
  nonbonded model="   0" pdb="HD13 LEU A 119 "
            model="   0" pdb=" OE1 GLU A 123 "
     model   vdw
     1.555 2.620
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.743 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.760 1.850
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.767 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.784 1.850
  ... (remaining 28501 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   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: "   0"
    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, 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: 0.98
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  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 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   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: "   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: 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.

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

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


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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 72
        1.23 -     1.43: 400
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.65e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.23e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.01e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.98e+00
  bond model="   0" pdb=" ND1 HIS A 134 "
       model="   0" pdb=" CE1 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.75e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.24 -   106.09: 93
      106.09 -   111.94: 2525
      111.94 -   117.80: 467
      117.80 -   123.65: 854
      123.65 -   129.50: 140
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  117.88    4.72 1.00e+00 1.00e+00 2.23e+01
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  129.50   -7.80 1.80e+00 3.09e-01 1.88e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.44    4.16 1.00e+00 1.00e+00 1.73e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.09    3.51 1.00e+00 1.00e+00 1.23e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.89    4.31 1.30e+00 5.92e-01 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.63: 925
       12.63 -    25.26: 75
       25.26 -    37.89: 15
       37.89 -    50.52: 15
       50.52 -    63.15: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.99   29.01     0      5.00e+00 4.00e-02 3.37e+01
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.98   17.02     0      5.00e+00 4.00e-02 1.16e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.04  -15.96     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 80
       0.049 -    0.096: 50
       0.096 -    0.143: 36
       0.143 -    0.191: 9
       0.191 -    0.238: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.57e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.42e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.082 2.00e-02 2.50e+03   3.27e-02 3.20e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.024 2.00e-02 2.50e+03   4.86e-02 2.36e+01
        model="   0" pdb=" CG  ASP A  36 "    0.084 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.030 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.043 2.00e-02 2.50e+03   1.63e-02 7.99e+00
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 115
        2.16 -     2.77: 4034
        2.77 -     3.38: 6051
        3.38 -     3.99: 7121
        3.99 -     4.60: 10904
  Nonbonded interactions: 28225
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.547 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.589 1.850
  nonbonded model="   0" pdb=" HE2 PHE A  15 "
            model="   0" pdb="HE21 GLN A  66 "
     model   vdw
     1.598 2.100
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.736 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.755 1.850
  ... (remaining 28220 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: 95
        1.23 -     1.43: 377
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.33e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.21e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.94e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.81e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.84e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.76 -   106.40: 118
      106.40 -   112.05: 2521
      112.05 -   117.69: 440
      117.69 -   123.34: 825
      123.34 -   128.98: 175
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  HIS A 135 "
        model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
      ideal   model   delta    sigma   weight residual
     113.80  109.72    4.08 1.00e+00 1.00e+00 1.67e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.55    4.05 1.00e+00 1.00e+00 1.64e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.21    4.99 1.30e+00 5.92e-01 1.47e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.12    3.48 1.00e+00 1.00e+00 1.21e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.73    4.47 1.30e+00 5.92e-01 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 970
       17.21 -    34.41: 47
       34.41 -    51.62: 13
       51.62 -    68.82: 1
       68.82 -    86.03: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.25   25.75     0      5.00e+00 4.00e-02 2.65e+01
  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  155.83   24.17     0      5.00e+00 4.00e-02 2.34e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.13   23.87     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.039: 75
       0.039 -    0.077: 43
       0.077 -    0.115: 31
       0.115 -    0.153: 24
       0.153 -    0.191: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.17e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality model="   0" pdb=" CA  PRO A 117 "
            model="   0" pdb=" N   PRO A 117 "
            model="   0" pdb=" C   PRO A 117 "
            model="   0" pdb=" CB  PRO A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.11e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.071 2.00e-02 2.50e+03   3.01e-02 2.72e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.059 2.00e-02 2.50e+03   2.32e-02 1.61e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.056 2.00e-02 2.50e+03   2.19e-02 1.44e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.34 -     1.99: 24
        1.99 -     2.64: 2765
        2.64 -     3.30: 6627
        3.30 -     3.95: 7730
        3.95 -     4.60: 11868
  Nonbonded interactions: 29014
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.339 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.726 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb=" HB3 ALA A 115 "
            model="   0" pdb=" HG2 GLU A 120 "
     model   vdw
     1.760 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.763 1.850
  ... (remaining 29009 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2224
          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}
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.542, 45.935, 72.764, 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: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (68.577, 53.207, 65.331, 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: 2224
  At special positions: 0
  Unit cell: (66.547, 47.49, 56.954, 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    1113      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, 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: 0.91
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.04 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 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  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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 5
        1.23 -     1.42: 459
        1.42 -     1.61: 668
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   GLN A 100 "
       model="   0" pdb=" N   LYS A 101 "
    ideal  model  delta    sigma   weight residual
    1.329  1.304  0.025 1.40e-02 5.10e+03 3.15e+00
  bond model="   0" pdb=" C   ARG A 127 "
       model="   0" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.024 1.40e-02 5.10e+03 2.97e+00
  bond model="   0" pdb=" C   HIS A 134 "
       model="   0" pdb=" N   HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.40e-02 5.10e+03 2.78e+00
  bond model="   0" pdb=" C   LEU A 132 "
       model="   0" pdb=" N   GLU A 133 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.16e+00
  bond model="   0" pdb=" C   THR A  20 "
       model="   0" pdb=" N   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.14e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.65 -   106.70: 48
      106.70 -   112.76: 2724
      112.76 -   118.81: 435
      118.81 -   124.86: 828
      124.86 -   130.92: 44
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.03   -5.03 3.00e+00 1.11e-01 2.81e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  123.03   -5.03 3.00e+00 1.11e-01 2.81e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  104.19    4.81 3.00e+00 1.11e-01 2.58e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.49   -4.49 3.00e+00 1.11e-01 2.24e+00
  angle model="   0" pdb=" C   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  104.73    4.27 3.00e+00 1.11e-01 2.03e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.87: 982
       14.87 -    29.74: 25
       29.74 -    44.61: 19
       44.61 -    59.48: 4
       59.48 -    74.35: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   68.08  -68.08     1      3.00e+01 1.11e-03 6.68e+00
  dihedral model="   0" pdb=" CB  GLU A  84 "
           model="   0" pdb=" CG  GLU A  84 "
           model="   0" pdb=" CD  GLU A  84 "
           model="   0" pdb=" OE1 GLU A  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   66.82  -66.82     1      3.00e+01 1.11e-03 6.47e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -105.65  -74.35     2      3.00e+01 1.11e-03 4.95e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 123
       0.027 -    0.054: 35
       0.054 -    0.081: 7
       0.081 -    0.107: 9
       0.107 -    0.134: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.13e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.54   -0.10 2.00e-01 2.50e+01 2.60e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.016 5.00e-02 4.00e+02   2.49e-02 9.96e-01
        model="   0" pdb=" N   PRO A   6 "   -0.043 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 137 "   -0.006 2.00e-02 2.50e+03   5.06e-03 5.13e-01
        model="   0" pdb=" CG  HIS A 137 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 137 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 137 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 137 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 137 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 137 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 137 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "    0.011 5.00e-02 4.00e+02   1.66e-02 4.39e-01
        model="   0" pdb=" N   PRO A  54 "   -0.029 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "    0.008 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "    0.009 5.00e-02 4.00e+02
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.29: 327
        2.29 -     2.87: 5146
        2.87 -     3.45: 5423
        3.45 -     4.02: 7172
        4.02 -     4.60: 10642
  Nonbonded interactions: 28710
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ2 LYS A  85 "
            model="   0" pdb=" OD2 ASP A  88 "
     model   vdw
     1.717 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.746 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.769 1.850
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.796 1.850
  nonbonded model="   0" pdb=" H   TYR A  91 "
            model="   0" pdb=" O   LEU A  99 "
     model   vdw
     1.826 1.850
  ... (remaining 28705 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.19, per 1000 atoms: 0.54
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (77.714, 46.326, 42.833, 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: 0.93, per 1000 atoms: 0.42
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.44, 56.473, 54.143, 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   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: "   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: 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.


  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 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: "   0"
    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: 54
        1.23 -     1.42: 418
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.78e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.37e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.34e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.26e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.68e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.27 -   106.05: 92
      106.05 -   111.82: 2494
      111.82 -   117.60: 484
      117.60 -   123.38: 839
      123.38 -   129.15: 170
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.87    3.73 1.00e+00 1.00e+00 1.39e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.23   -3.63 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.04    3.56 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.15   -4.75 1.40e+00 5.10e-01 1.15e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.80    4.40 1.30e+00 5.92e-01 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 974
       17.48 -    34.96: 46
       34.96 -    52.44: 9
       52.44 -    69.91: 3
       69.91 -    87.39: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" C   ASP A 116 "
           model="   0" pdb=" N   PRO A 117 "
           model="   0" pdb=" CA  PRO A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.48  -17.52     0      5.00e+00 4.00e-02 1.23e+01
  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  163.12   16.88     0      5.00e+00 4.00e-02 1.14e+01
  dihedral model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" CB  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.78    8.18     0      2.50e+00 1.60e-01 1.07e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 84
       0.054 -    0.107: 59
       0.107 -    0.161: 26
       0.161 -    0.214: 6
       0.214 -    0.268: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.93e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.51e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.052 2.00e-02 2.50e+03   2.43e-02 1.77e+01
        model="   0" pdb=" CG  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.019 2.00e-02 2.50e+03   3.91e-02 1.53e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.068 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.023 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.058 2.00e-02 2.50e+03   2.26e-02 1.53e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.006 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 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 265
        2.27 -     2.85: 5050
        2.85 -     3.44: 5463
        3.44 -     4.02: 7246
        4.02 -     4.60: 10738
  Nonbonded interactions: 28762
  Sorted by model distance:
  nonbonded model="   0" pdb=" HG1 THR A  82 "
            model="   0" pdb=" O   ASP A  88 "
     model   vdw
     1.689 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.754 1.850
  ... (remaining 28757 not shown)

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

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

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (40.643, 44.397, 77.709, 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 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.

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...
  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 -     1.23: 57
        1.23 -     1.42: 415
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.15e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.97e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.24e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.17e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.99e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.13 -   105.93: 72
      105.93 -   111.72: 2514
      111.72 -   117.52: 479
      117.52 -   123.31: 834
      123.31 -   129.11: 180
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.66    3.94 1.00e+00 1.00e+00 1.55e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.05    3.55 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.10   -3.50 1.00e+00 1.00e+00 1.23e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.89   -4.49 1.40e+00 5.10e-01 1.03e+01
  angle model="   0" pdb=" CA  TYR A  81 "
        model="   0" pdb=" CB  TYR A  81 "
        model="   0" pdb=" CG  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     113.90  108.35    5.55 1.80e+00 3.09e-01 9.51e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 973
       17.82 -    35.64: 47
       35.64 -    53.47: 10
       53.47 -    71.29: 2
       71.29 -    89.11: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.27  -27.73     0      5.00e+00 4.00e-02 3.08e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.53  -18.47     0      5.00e+00 4.00e-02 1.36e+01
  dihedral model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" CB  TYR A  81 "
           model="   0" pdb=" CG  TYR A  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -108.68   48.68     3      1.50e+01 4.44e-03 8.67e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 76
       0.046 -    0.091: 50
       0.091 -    0.136: 35
       0.136 -    0.182: 12
       0.182 -    0.227: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality model="   0" pdb=" CA  GLU A  84 "
            model="   0" pdb=" N   GLU A  84 "
            model="   0" pdb=" C   GLU A  84 "
            model="   0" pdb=" CB  GLU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.13e-01
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.12e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.272 2.00e-02 2.50e+03   1.11e-01 3.70e+02
        model="   0" pdb=" CG  TYR A  81 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.060 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.201 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.089 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.099 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.043 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.071 2.00e-02 2.50e+03   2.84e-02 2.43e+01
        model="   0" pdb=" CG  TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.010 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.039 2.00e-02 2.50e+03   2.03e-02 1.24e+01
        model="   0" pdb=" CG  TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 359
        2.30 -     2.87: 5147
        2.87 -     3.45: 5414
        3.45 -     4.02: 7236
        4.02 -     4.60: 10643
  Nonbonded interactions: 28799
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.721 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.730 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.740 1.850
  nonbonded model="   0" pdb=" HE1 HIS A  43 "
            model="   0" pdb=" O   TYR A 111 "
     model   vdw
     1.782 2.450
  ... (remaining 28794 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)----------                  

  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.087, 48.378, 60.422, 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: 1.02
  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.

        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: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  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 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: 90
        1.23 -     1.43: 382
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.37e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.378 -0.024 1.10e-02 8.26e+03 4.93e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.302  0.028 1.30e-02 5.92e+03 4.79e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.78e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.77e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   106.24: 108
      106.24 -   111.93: 2509
      111.93 -   117.63: 460
      117.63 -   123.32: 823
      123.32 -   129.02: 179
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.02    5.18 1.30e+00 5.92e-01 1.59e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.30   -3.70 1.00e+00 1.00e+00 1.37e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.01    3.59 1.00e+00 1.00e+00 1.29e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.02    3.58 1.00e+00 1.00e+00 1.28e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.76    4.44 1.30e+00 5.92e-01 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 989
       16.80 -    33.60: 28
       33.60 -    50.41: 12
       50.41 -    67.21: 3
       67.21 -    84.01: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.12   36.88     0      5.00e+00 4.00e-02 5.44e+01
  dihedral model="   0" pdb=" CA  GLY A  87 "
           model="   0" pdb=" C   GLY A  87 "
           model="   0" pdb=" N   ASP A  88 "
           model="   0" pdb=" CA  ASP A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.83  -21.17     0      5.00e+00 4.00e-02 1.79e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.25   17.75     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 74
       0.039 -    0.078: 43
       0.078 -    0.117: 38
       0.117 -    0.156: 18
       0.156 -    0.195: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.49e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.15e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.62e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.090 2.00e-02 2.50e+03   3.81e-02 4.36e+01
        model="   0" pdb=" CG  TYR A  81 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.062 2.00e-02 2.50e+03   2.43e-02 1.77e+01
        model="   0" pdb=" CG  TYR A  89 "    0.010 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 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.056 2.00e-02 2.50e+03   2.19e-02 1.44e+01
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.005 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 "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.01 -     1.73: 9
        1.73 -     2.44: 1247
        2.44 -     3.16: 6885
        3.16 -     3.88: 8361
        3.88 -     4.60: 13239
  Nonbonded interactions: 29741
  Sorted by model distance:
  nonbonded model="   0" pdb=" H3  MET A   1 "
            model="   0" pdb=" HD2 HIS A 135 "
     model   vdw
     1.006 2.100
  nonbonded model="   0" pdb=" HE1 TYR A  81 "
            model="   0" pdb=" HD2 TYR A  91 "
     model   vdw
     1.338 2.100
  nonbonded model="   0" pdb=" OH  TYR A  81 "
            model="   0" pdb=" HB3 TYR A  91 "
     model   vdw
     1.437 2.620
  nonbonded model="   0" pdb=" H1  MET A   1 "
            model="   0" pdb=" HD2 HIS A 135 "
     model   vdw
     1.438 2.100
  nonbonded model="   0" pdb=" HH  TYR A  81 "
            model="   0" pdb=" HB3 TYR A  91 "
     model   vdw
     1.442 2.270
  ... (remaining 29736 not shown)

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

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


  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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1113
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" CZ  ARG A 127 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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="   0" pdb=" CZ  ARG A  21 "
       model="   0" 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="   0" pdb=" NE  ARG A  21 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       80.78 -    90.80: 1
       90.80 -   100.83: 0
      100.83 -   110.85: 2512
      110.85 -   120.88: 1136
      120.88 -   130.90: 442
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   80.78   28.69 3.00e+00 1.11e-01 9.15e+01
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  123.29  -13.82 3.00e+00 1.11e-01 2.12e+01
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.17   -9.70 3.00e+00 1.11e-01 1.05e+01
  angle model="   0" pdb=" CA  GLY A  80 "
        model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" H   GLY A  80 "
      ideal   model   delta    sigma   weight residual
     114.00  119.90   -5.90 3.00e+00 1.11e-01 3.87e+00
  angle model="   0" pdb=" CA  GLY A 121 "
        model="   0" pdb=" N   GLY A 121 "
        model="   0" pdb=" H   GLY A 121 "
      ideal   model   delta    sigma   weight residual
     114.00  119.89   -5.89 3.00e+00 1.11e-01 3.86e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 819
       17.58 -    35.15: 105
       35.15 -    52.72: 70
       52.72 -    70.30: 35
       70.30 -    87.87: 10
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" 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="   0" pdb=" CB  LYS A  79 "
           model="   0" pdb=" CG  LYS A  79 "
           model="   0" pdb=" CD  LYS A  79 "
           model="   0" 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="   0" pdb=" CG  LYS A  27 "
           model="   0" pdb=" CD  LYS A  27 "
           model="   0" pdb=" CE  LYS A  27 "
           model="   0" 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 1036 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
       Symmetry information was not found, putting molecule in P1 box.

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

0.076 -    0.095: 19
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  30 "
            model="   0" pdb=" N   ILE A  30 "
            model="   0" pdb=" C   ILE A  30 "
            model="   0" 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="   0" pdb=" CA  ILE A  38 "
            model="   0" pdb=" N   ILE A  38 "
            model="   0" pdb=" C   ILE A  38 "
            model="   0" 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="   0" pdb=" CA  ILE A  37 "
            model="   0" pdb=" N   ILE A  37 "
            model="   0" pdb=" C   ILE A  37 "
            model="   0" 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="   0" pdb=" CB  TYR A 111 "   -0.001 2.00e-02 2.50e+03   6.58e-04 1.30e-02
        model="   0" pdb=" CG  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.000 2.00e-02 2.50e+03   5.75e-04 9.92e-03
        model="   0" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "   -0.000 2.00e-02 2.50e+03   5.19e-04 8.10e-03
        model="   0" pdb=" CG  TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.45: 1304
        2.45 -     2.99: 5143
        2.99 -     3.53: 5452
        3.53 -     4.06: 6747
        4.06 -     4.60: 9849
  Nonbonded interactions: 28495
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   THR A  56 "
            model="   0" pdb=" H   ALA A  60 "
     model   vdw
     1.913 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.913 1.850
  nonbonded model="   0" pdb=" O   LEU A   9 "
            model="   0" pdb=" H   SER A  13 "
     model   vdw
     1.916 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.922 1.850
  nonbonded model="   0" pdb=" H   SER A  76 "
            model="   0" pdb=" H   ILE A  77 "
     model   vdw
     1.968 2.100
  ... (remaining 28490 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: 1
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.337 -0.016 1.00e-02 1.00e+04 2.64e+00
  bond model="   0" pdb=" C   PRO A  22 "
       model="   0" pdb=" N   ASP A  23 "
    ideal  model  delta    sigma   weight residual
    1.329  1.348 -0.019 1.40e-02 5.10e+03 1.86e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.348 -0.019 1.40e-02 5.10e+03 1.80e+00
  bond model="   0" pdb=" C   ASP A  29 "
       model="   0" pdb=" N   ILE A  30 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.74e+00
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.465  0.026 2.10e-02 2.27e+03 1.50e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.74 -   106.79: 58
      106.79 -   112.84: 2708
      112.84 -   118.89: 437
      118.89 -   124.94: 834
      124.94 -   130.98: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.96    5.04 3.00e+00 1.11e-01 2.82e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.03   -5.03 3.00e+00 1.11e-01 2.81e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  104.09    4.91 3.00e+00 1.11e-01 2.68e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.58   -4.58 3.00e+00 1.11e-01 2.33e+00
  angle model="   0" pdb=" C   PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  104.49    4.51 3.00e+00 1.11e-01 2.26e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.68: 996
       16.68 -    33.37: 25
       33.37 -    50.05: 8
       50.05 -    66.73: 2
       66.73 -    83.42: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.42   83.42     1      3.00e+01 1.11e-03 9.44e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -100.84  -79.16     2      3.00e+01 1.11e-03 5.14e+00
  dihedral model="   0" pdb=" CB  GLU A  16 "
           model="   0" pdb=" CG  GLU A  16 "
           model="   0" pdb=" CD  GLU A  16 "
           model="   0" pdb=" OE1 GLU A  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -50.77   50.77     1      3.00e+01 1.11e-03 3.92e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 105
       0.029 -    0.057: 55
       0.057 -    0.086: 7
       0.086 -    0.114: 6
       0.114 -    0.142: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.06e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.001 2.00e-02 2.50e+03   5.16e-03 7.99e-01
        model="   0" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.003 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 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.002 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 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.013 5.00e-02 4.00e+02   2.01e-02 6.48e-01
        model="   0" pdb=" N   PRO A   6 "   -0.035 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.010 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.011 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.007 2.00e-02 2.50e+03   4.15e-03 5.17e-01
        model="   0" pdb=" CG  TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.34: 530
        2.34 -     2.91: 5113
        2.91 -     3.47: 5328
        3.47 -     4.04: 7176
        4.04 -     4.60: 10374
  Nonbonded interactions: 28521
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.776 1.850
  nonbonded model="   0" pdb=" HE  ARG A  21 "
            model="   0" pdb=" OD2 ASP A  29 "
     model   vdw
     1.786 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.786 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.806 1.850
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.822 1.850
  ... (remaining 28516 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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.76, per 1000 atoms: 0.34
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.052, 52.518, 51.835, 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: 0.71
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.78 seconds

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


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

  Time building chain proxies: 1.20, per 1000 atoms: 0.54
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.875, 41.479, 56.251, 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     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: 1113
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" CZ  ARG A 127 "
       model="   0" 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="   0" pdb=" NE  ARG A  58 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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="   0" pdb=" CZ  ARG A  58 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       65.09 -    78.25: 1
       78.25 -    91.41: 0
       91.41 -   104.58: 16
      104.58 -   117.74: 2998
      117.74 -   130.90: 1076
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   65.09   44.38 3.00e+00 1.11e-01 2.19e+02
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  130.03  -20.56 3.00e+00 1.11e-01 4.69e+01
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.16   -9.69 3.00e+00 1.11e-01 1.04e+01
  angle model="   0" pdb=" CA  GLY A  87 "
        model="   0" pdb=" N   GLY A  87 "
        model="   0" pdb=" H   GLY A  87 "
      ideal   model   delta    sigma   weight residual
     114.00  119.92   -5.92 3.00e+00 1.11e-01 3.90e+00
  angle model="   0" pdb=" CA  GLY A  42 "
        model="   0" pdb=" N   GLY A  42 "
        model="   0" pdb=" H   GLY A  42 "
      ideal   model   delta    sigma   weight residual
     114.00  119.90   -5.90 3.00e+00 1.11e-01 3.87e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 809
       17.73 -    35.46: 107
       35.46 -    53.19: 88
       53.19 -    70.92: 26
       70.92 -    88.65: 9
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  24 "
           model="   0" pdb=" CG  GLU A  24 "
           model="   0" pdb=" CD  GLU A  24 "
           model="   0" 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="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" CB  ASP A 116 "
           model="   0" 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="   0" pdb=" CA  GLU A 123 "
           model="   0" pdb=" CB  GLU A 123 "
           model="   0" pdb=" CG  GLU A 123 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" 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="   0" pdb=" CA  ILE A  77 "
            model="   0" pdb=" N   ILE A  77 "
            model="   0" pdb=" C   ILE A  77 "
            model="   0" 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="   0" pdb=" CA  ILE A  38 "
            model="   0" pdb=" N   ILE A  38 "
            model="   0" pdb=" C   ILE A  38 "
            model="   0" 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="   0" pdb=" CB  TYR A 105 "   -0.000 2.00e-02 2.50e+03   7.72e-04 1.79e-02
        model="   0" pdb=" CG  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.000 2.00e-02 2.50e+03   6.27e-04 1.18e-02
        model="   0" pdb=" CG  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.000 2.00e-02 2.50e+03   5.88e-04 1.04e-02
        model="   0" pdb=" CG  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.45: 1286
        2.45 -     2.99: 5205
        2.99 -     3.52: 5521
        3.52 -     4.06: 6981
        4.06 -     4.60: 9791
  Nonbonded interactions: 28784
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   PRO A 117 "
            model="   0" pdb=" H   LEU A 119 "
     model   vdw
     1.912 1.850
  nonbonded model="   0" pdb=" O   LEU A   9 "
            model="   0" pdb=" H   SER A  13 "
     model   vdw
     1.915 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.932 1.850
  nonbonded model="   0" pdb=" O   THR A  56 "
            model="   0" pdb=" H   ALA A  60 "
     model   vdw
     1.967 1.850
  nonbonded model="   0" pdb=" HB2 PRO A 117 "
            model="   0" pdb=" H   ASP A 118 "
     model   vdw
     1.974 2.270
  ... (remaining 28779 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: 0.98
  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.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 60
        1.23 -     1.43: 412
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.33e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.83e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 5.80e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.51e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.21e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.99 -   105.75: 71
      105.75 -   111.50: 2413
      111.50 -   117.25: 569
      117.25 -   123.01: 787
      123.01 -   128.76: 239
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.38    4.22 1.00e+00 1.00e+00 1.78e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.41   -3.81 1.00e+00 1.00e+00 1.45e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.03    3.57 1.00e+00 1.00e+00 1.27e+01
  angle model="   0" pdb=" NE  ARG A  58 "
        model="   0" pdb=" CZ  ARG A  58 "
        model="   0" pdb=" NH2 ARG A  58 "
      ideal   model   delta    sigma   weight residual
     119.20  122.19   -2.99 9.00e-01 1.23e+00 1.10e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.98    4.22 1.30e+00 5.92e-01 1.05e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 981
       17.46 -    34.92: 39
       34.92 -    52.39: 12
       52.39 -    69.85: 0
       69.85 -    87.31: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.82   19.18     0      5.00e+00 4.00e-02 1.47e+01
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.11   17.89     0      5.00e+00 4.00e-02 1.28e+01
  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  162.79   17.21     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 73
       0.041 -    0.082: 50
       0.082 -    0.123: 31
       0.123 -    0.164: 19
       0.164 -    0.205: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.70e-01
  chirality model="   0" pdb=" CA  HIS A 135 "
            model="   0" pdb=" N   HIS A 135 "
            model="   0" pdb=" C   HIS A 135 "
            model="   0" pdb=" CB  HIS A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.43e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.067 2.00e-02 2.50e+03   2.70e-02 2.18e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.067 2.00e-02 2.50e+03   2.67e-02 2.14e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.016 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 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.007 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 "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.010 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.052 2.00e-02 2.50e+03   2.30e-02 1.59e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 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 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 126
        2.19 -     2.79: 4257
        2.79 -     3.40: 5963
        3.40 -     4.00: 7066
        4.00 -     4.60: 10615
  Nonbonded interactions: 28027
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.589 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.715 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.734 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.737 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.751 1.850
  ... (remaining 28022 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:    0.038 (Z=  2.365)
  Mean delta:    0.012 (Z=  0.606)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   129.42    -7.72  1.80e+00  1.84e+01   4.3*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

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.717 (Z=  4.287)
  Mean delta:    1.609 (Z=  0.875)

                      ----------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   156.53    23.47  5.00e+00  2.20e+01   4.7*sigma

  Min. delta:    0.001
  Max. delta:   85.038
  Mean delta:   11.624

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.204
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.071
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.431
    Angle     :  1.551   7.717   4079  Z= 0.669
    Chirality :  0.076   0.204    176
    Planarity :  0.008   0.053    327
    Dihedral  : 10.867  85.038    769
    Min Nonbonded Distance : 1.607
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  4.03 %
      Favored  : 95.16 %
    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:  0.01 (0.71), residues: 137
    helix:  0.13 (0.51), residues: 81
    sheet:  None (None), residues: 0
    loop :  0.05 (0.96), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.010   0.003   PHE A  45 
   TYR   0.068   0.012   TYR A 111 
   ARG   0.057   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.005   0.002   PHE A  67 
   TYR   0.057   0.014   TYR A 111 
   ARG   0.007   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.609, 52.088, 63.754, 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 =  94.16 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.55
  MolProbity score      =   1.71

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: 1.01
  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.

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, 2224
          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: 1.01
  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.

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: 85
        1.23 -     1.43: 387
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.68e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.93e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.75e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.28e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.25e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.39 -   106.05: 95
      106.05 -   111.72: 2465
      111.72 -   117.38: 509
      117.38 -   123.05: 770
      123.05 -   128.71: 240
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.55    4.05 1.00e+00 1.00e+00 1.64e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.04    3.56 1.00e+00 1.00e+00 1.27e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.68    4.52 1.30e+00 5.92e-01 1.21e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.81    4.39 1.30e+00 5.92e-01 1.14e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.82    4.38 1.30e+00 5.92e-01 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 968
       17.71 -    35.42: 47
       35.42 -    53.14: 14
       53.14 -    70.85: 2
       70.85 -    88.56: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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  155.50   24.50     0      5.00e+00 4.00e-02 2.40e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.99  -19.01     0      5.00e+00 4.00e-02 1.45e+01
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.56  -15.44     0      5.00e+00 4.00e-02 9.53e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.039: 82
       0.039 -    0.078: 34
       0.078 -    0.117: 38
       0.117 -    0.155: 19
       0.155 -    0.194: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.41e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.20e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.33e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.066 2.00e-02 2.50e+03   2.60e-02 2.03e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.059 2.00e-02 2.50e+03   2.56e-02 1.97e+01
        model="   0" pdb=" CG  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.012 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 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.049 2.00e-02 2.50e+03   1.83e-02 1.01e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.015 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 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 213
        2.23 -     2.82: 4660
        2.82 -     3.42: 5914
        3.42 -     4.01: 7357
        4.01 -     4.60: 11102
  Nonbonded interactions: 29246
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.639 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.721 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.725 1.850
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.763 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  49 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.764 1.850
  ... (remaining 29241 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: 99
        1.23 -     1.43: 373
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.49e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.10e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.360 -0.031 1.40e-02 5.10e+03 5.05e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 5.01e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 4.83e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.22 -   106.75: 168
      106.75 -   112.28: 2495
      112.28 -   117.82: 426
      117.82 -   123.35: 814
      123.35 -   128.88: 176
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.69    3.91 1.00e+00 1.00e+00 1.53e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.38   -3.78 1.00e+00 1.00e+00 1.43e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.94   -3.34 1.00e+00 1.00e+00 1.12e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.33    3.27 1.00e+00 1.00e+00 1.07e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.97    4.23 1.30e+00 5.92e-01 1.06e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 967
       17.42 -    34.84: 44
       34.84 -    52.26: 16
       52.26 -    69.68: 4
       69.68 -    87.10: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.78   36.22     0      5.00e+00 4.00e-02 5.25e+01
  dihedral model="   0" pdb=" CA  HIS A 135 "
           model="   0" pdb=" C   HIS A 135 "
           model="   0" pdb=" N   HIS A 136 "
           model="   0" pdb=" CA  HIS A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.08   26.92     0      5.00e+00 4.00e-02 2.90e+01
  dihedral model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" C   HIS A 137 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.46   24.54     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 73
       0.039 -    0.079: 46
       0.079 -    0.118: 37
       0.118 -    0.157: 18
       0.157 -    0.197: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.66e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.50e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.020 2.00e-02 2.50e+03   4.06e-02 1.65e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.070 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.024 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.057 2.00e-02 2.50e+03   2.21e-02 1.47e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.053 2.00e-02 2.50e+03   2.20e-02 1.45e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.011 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 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 112
        2.15 -     2.76: 4008
        2.76 -     3.37: 6217
        3.37 -     3.99: 7442
        3.99 -     4.60: 11196
  Nonbonded interactions: 28975
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE1 TYR A  81 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.532 2.100
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.618 1.850
  nonbonded model="   0" pdb=" HH  TYR A  81 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.656 2.100
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.659 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  49 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.667 1.850
  ... (remaining 28970 not shown)

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

  Symmetric amino acids flipped
    Residue "A TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A ASP   44": "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: 1.04
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 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: 0.96, per 1000 atoms: 0.43
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.415, 63.479, 65.796, 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: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2224
  At special positions: 0
  Unit cell: (50.175, 60.425, 58.535, 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    1113      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:    0.039 (Z=  2.617)
  Mean delta:    0.012 (Z=  0.610)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.31     4.29  1.00e+00  1.84e+01   4.3*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    6.642 (Z=  4.288)
  Mean delta:    1.575 (Z=  0.856)

                      ----------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   158.65    21.35  5.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.042
  Max. delta:   86.935
  Mean delta:   12.414

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.196
  Mean delta:    0.075

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.053
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.434
    Angle     :  1.526   6.642   4079  Z= 0.657
    Chirality :  0.075   0.196    176
    Planarity :  0.008   0.039    327
    Dihedral  : 11.084  86.935    769
    Min Nonbonded Distance : 1.713
  
  Molprobity Statistics.
    All-atom Clashscore : 7.21
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  0.73 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  3.23 %
      Favored  : 95.16 %
    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:  1.12 (0.70), residues: 137
    helix:  0.40 (0.51), residues: 82
    sheet: -1.10 (1.07), residues: 10
    loop :  2.38 (1.06), residues: 45
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.066   0.009   TYR A  50 
   ARG   0.042   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.008   0.003   PHE A  67 
   TYR   0.054   0.011   TYR A  50 
   ARG   0.006   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 36
        1.23 -     1.42: 436
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.57e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.58e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.68e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.76e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.73e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.62 -   105.49: 44
      105.49 -   111.35: 2421
      111.35 -   117.21: 591
      117.21 -   123.08: 806
      123.08 -   128.94: 217
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.71    3.89 1.00e+00 1.00e+00 1.51e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.12    3.48 1.00e+00 1.00e+00 1.21e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  127.21    3.99 1.30e+00 5.92e-01 9.42e+00
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.67   -4.27 1.40e+00 5.10e-01 9.30e+00
  angle model="   0" pdb=" N   PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" CB  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     103.00  106.31   -3.31 1.10e+00 8.26e-01 9.06e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 970
       16.90 -    33.81: 46
       33.81 -    50.71: 14
       50.71 -    67.61: 2
       67.61 -    84.51: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  161.27   18.73     0      5.00e+00 4.00e-02 1.40e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.86   17.14     0      5.00e+00 4.00e-02 1.18e+01
  dihedral model="   0" pdb=" CA  ALA A  48 "
           model="   0" pdb=" C   ALA A  48 "
           model="   0" pdb=" N   GLU A  49 "
           model="   0" pdb=" CA  GLU A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.67   15.33     0      5.00e+00 4.00e-02 9.40e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.045: 77
       0.045 -    0.090: 57
       0.090 -    0.135: 33
       0.135 -    0.180: 7
       0.180 -    0.225: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    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="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.49e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.066 2.00e-02 2.50e+03   2.60e-02 2.02e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.051 2.00e-02 2.50e+03   2.00e-02 1.20e+01
        model="   0" pdb=" CG  TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.005 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 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.017 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.47e+00
        model="   0" pdb=" CG  ASP A  36 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 181
        2.21 -     2.81: 4470
        2.81 -     3.40: 5955
        3.40 -     4.00: 7391
        4.00 -     4.60: 11180
  Nonbonded interactions: 29177
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A   8 "
            model="   0" pdb="HH21 ARG A  58 "
     model   vdw
     1.611 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.662 1.850
  nonbonded model="   0" pdb=" HE2 PHE A  45 "
            model="   0" pdb=" HE1 MET A 128 "
     model   vdw
     1.699 2.270
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.741 1.850
  nonbonded model="   0" pdb="HG23 THR A  82 "
            model="   0" pdb=" HB3 SER A  90 "
     model   vdw
     1.777 2.440
  ... (remaining 29172 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   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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.73 %
                favored =  98.54 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   7.21
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.53
  MolProbity score      =   1.55

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: 1.03
  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.

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: 1.21
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.33 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: 52
        1.23 -     1.42: 420
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD  GLU A  32 "
       model="   0" pdb=" OE1 GLU A  32 "
    ideal  model  delta    sigma   weight residual
    1.249  1.195  0.054 1.90e-02 2.77e+03 8.09e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.28e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 5.97e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.39e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 5.02e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.91 -   106.48: 129
      106.48 -   112.06: 2500
      112.06 -   117.63: 454
      117.63 -   123.20: 793
      123.20 -   128.78: 203
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  GLU A  32 "
        model="   0" pdb=" CG  GLU A  32 "
        model="   0" pdb=" CD  GLU A  32 "
      ideal   model   delta    sigma   weight residual
     112.60  119.46   -6.86 1.70e+00 3.46e-01 1.63e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.76    3.84 1.00e+00 1.00e+00 1.47e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.52    4.68 1.30e+00 5.92e-01 1.29e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.70    4.50 1.30e+00 5.92e-01 1.20e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.16    3.44 1.00e+00 1.00e+00 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 976
       17.33 -    34.66: 42
       34.66 -    51.99: 11
       51.99 -    69.32: 3
       69.32 -    86.65: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.73  -21.27     0      5.00e+00 4.00e-02 1.81e+01
  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  160.16   19.84     0      5.00e+00 4.00e-02 1.57e+01
  dihedral model="   0" pdb=" CA  VAL A 112 "
           model="   0" pdb=" C   VAL A 112 "
           model="   0" pdb=" N   LYS A 113 "
           model="   0" pdb=" CA  LYS A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.63   18.37     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 76
       0.040 -    0.080: 44
       0.080 -    0.119: 32
       0.119 -    0.159: 19
       0.159 -    0.199: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.88e-01
  chirality model="   0" pdb=" CA  ASP A 116 "
            model="   0" pdb=" N   ASP A 116 "
            model="   0" pdb=" C   ASP A 116 "
            model="   0" pdb=" CB  ASP A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.21e-01
  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    2.34    0.17 2.00e-01 2.50e+01 7.02e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.066 2.00e-02 2.50e+03   2.91e-02 2.54e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.068 2.00e-02 2.50e+03   2.68e-02 2.15e+01
        model="   0" pdb=" CG  TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.057 2.00e-02 2.50e+03   2.29e-02 1.58e+01
        model="   0" pdb=" CG  TYR A  89 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        0.88 -     1.62: 7
        1.62 -     2.37: 735
        2.37 -     3.11: 6895
        3.11 -     3.86: 8407
        3.86 -     4.60: 13108
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 29152
  Sorted by model distance:
  nonbonded model="   0" pdb=" HG3 GLU A  32 "
            model="   0" pdb=" HZ1 LYS A  85 "
     model   vdw
     0.878 2.270
  nonbonded model="   0" pdb=" HG2 GLU A  32 "
            model="   0" pdb=" HZ3 LYS A  85 "
     model   vdw
     1.225 2.270
  nonbonded model="   0" pdb=" OE2 GLU A  32 "
            model="   0" pdb=" HE2 LYS A  85 "
     model   vdw
     1.384 2.620
  nonbonded model="   0" pdb=" HB  ILE A  86 "
            model="   0" pdb=" HE2 TYR A  89 "
     model   vdw
     1.474 2.270
  nonbonded model="   0" pdb=" HG3 GLU A  32 "
            model="   0" pdb=" NZ  LYS A  85 "
     model   vdw
     1.479 2.770
  ... (remaining 29147 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 -     1.43: 404
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 8.75e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.57e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.87e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.72e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.69e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.02 -   106.02: 94
      106.02 -   112.01: 2518
      112.01 -   118.00: 497
      118.00 -   123.99: 875
      123.99 -   129.98: 95
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  129.98   -8.28 1.80e+00 3.09e-01 2.12e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.49    4.11 1.00e+00 1.00e+00 1.69e+01
  angle model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
        model="   0" pdb=" CB  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     111.50  105.53    5.97 1.70e+00 3.46e-01 1.23e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.15    3.45 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.74    4.46 1.30e+00 5.92e-01 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 966
       17.28 -    34.57: 47
       34.57 -    51.85: 15
       51.85 -    69.13: 3
       69.13 -    86.41: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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  137.07   42.93     0      5.00e+00 4.00e-02 7.37e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.48  -30.52     0      5.00e+00 4.00e-02 3.73e+01
  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  153.84   26.16     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.055: 84
       0.055 -    0.108: 57
       0.108 -    0.162: 29
       0.162 -    0.216: 5
       0.216 -    0.269: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.28e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.058 2.00e-02 2.50e+03   2.26e-02 1.53e+01
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.005 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 "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.059 2.00e-02 2.50e+03   2.23e-02 1.49e+01
        model="   0" pdb=" CG  TYR A  81 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.055 2.00e-02 2.50e+03   2.19e-02 1.44e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 344
        2.30 -     2.87: 5171
        2.87 -     3.45: 5357
        3.45 -     4.02: 7162
        4.02 -     4.60: 10527
  Nonbonded interactions: 28561
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.722 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb=" O   ILE A  78 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.785 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.796 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.802 1.850
  ... (remaining 28556 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}

  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: 1.07 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}
  Time building chain proxies: 0.92, per 1000 atoms: 0.41
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.134, 53.062, 68.092, 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: 123
        1.23 -     1.43: 349
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.19e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.05e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.45e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.42e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.31e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.33 -   106.45: 108
      106.45 -   112.57: 2609
      112.57 -   118.68: 458
      118.68 -   124.80: 849
      124.80 -   130.92: 55
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.62    3.98 1.00e+00 1.00e+00 1.59e+01
  angle model="   0" pdb=" CB  HIS A 138 "
        model="   0" pdb=" CG  HIS A 138 "
        model="   0" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  126.13    5.07 1.30e+00 5.92e-01 1.52e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.18    3.42 1.00e+00 1.00e+00 1.17e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.01   -4.61 1.40e+00 5.10e-01 1.09e+01
  angle model="   0" pdb=" CA  ASP A 116 "
        model="   0" pdb=" CB  ASP A 116 "
        model="   0" pdb=" CG  ASP A 116 "
      ideal   model   delta    sigma   weight residual
     112.60  115.61   -3.01 1.00e+00 1.00e+00 9.06e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 969
       17.09 -    34.18: 46
       34.18 -    51.28: 10
       51.28 -    68.37: 6
       68.37 -    85.46: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" C   ASP A 116 "
           model="   0" pdb=" N   PRO A 117 "
           model="   0" pdb=" CA  PRO A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.49  -24.51     0      5.00e+00 4.00e-02 2.40e+01
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.81   22.19     0      5.00e+00 4.00e-02 1.97e+01
  dihedral model="   0" pdb=" CA  PRO A 117 "
           model="   0" pdb=" C   PRO A 117 "
           model="   0" pdb=" N   ASP A 118 "
           model="   0" pdb=" CA  ASP A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.62  -21.38     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 92
       0.046 -    0.093: 47
       0.093 -    0.139: 32
       0.139 -    0.185: 3
       0.185 -    0.232: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PRO A 117 "
            model="   0" pdb=" N   PRO A 117 "
            model="   0" pdb=" C   PRO A 117 "
            model="   0" pdb=" CB  PRO A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  ASP A 118 "
            model="   0" pdb=" N   ASP A 118 "
            model="   0" pdb=" C   ASP A 118 "
            model="   0" pdb=" CB  ASP A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.78e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.41e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.085 2.00e-02 2.50e+03   3.40e-02 3.46e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A  43 "   -0.038 2.00e-02 2.50e+03   2.30e-02 1.06e+01
        model="   0" pdb=" CG  HIS A  43 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  45 "    0.044 2.00e-02 2.50e+03   1.68e-02 8.52e+00
        model="   0" pdb=" CG  PHE A  45 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  45 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  45 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  45 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  45 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  45 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  45 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  45 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  45 "    0.018 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 178
        2.21 -     2.81: 4475
        2.81 -     3.41: 5868
        3.41 -     4.00: 7257
        4.00 -     4.60: 10888
  Nonbonded interactions: 28666
  Sorted by model distance:
  nonbonded model="   0" pdb="HG12 VAL A  41 "
            model="   0" pdb=" HD2 HIS A  43 "
     model   vdw
     1.616 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.681 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.702 1.850
  nonbonded model="   0" pdb=" HB3 PHE A  45 "
            model="   0" pdb="HD13 ILE A  51 "
     model   vdw
     1.760 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.761 1.850
  ... (remaining 28661 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 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: "   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: 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.


  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: "   0"
    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}

  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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      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: (54.308, 45.956, 54.619, 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: 54
        1.23 -     1.42: 418
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.87e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.61e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.19e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.03e+00
  bond model="   0" pdb=" ND1 HIS A 134 "
       model="   0" pdb=" CE1 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.34e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.90 -   105.74: 61
      105.74 -   111.58: 2473
      111.58 -   117.41: 531
      117.41 -   123.25: 822
      123.25 -   129.09: 192
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.74    3.86 1.00e+00 1.00e+00 1.49e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.86    3.74 1.00e+00 1.00e+00 1.40e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.89    3.71 1.00e+00 1.00e+00 1.38e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.12   -3.52 1.00e+00 1.00e+00 1.24e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.64    4.56 1.30e+00 5.92e-01 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.57: 971
       16.57 -    33.13: 45
       33.13 -    49.70: 11
       49.70 -    66.27: 4
       66.27 -    82.84: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  158.80   21.20     0      5.00e+00 4.00e-02 1.80e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.22   14.78     0      5.00e+00 4.00e-02 8.74e+00
  dihedral model="   0" pdb=" CA  ASP A  44 "
           model="   0" pdb=" C   ASP A  44 "
           model="   0" pdb=" N   PHE A  45 "
           model="   0" pdb=" CA  PHE A  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.42   14.58     0      5.00e+00 4.00e-02 8.51e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 90
       0.055 -    0.110: 54
       0.110 -    0.164: 30
       0.164 -    0.219: 1
       0.219 -    0.274: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" C   THR A  82 "
            model="   0" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.32e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "   -0.104 2.00e-02 2.50e+03   4.68e-02 6.58e+01
        model="   0" pdb=" CG  TYR A  68 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "   -0.095 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "    0.029 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.072 2.00e-02 2.50e+03   2.95e-02 2.61e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.018 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.063 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.21 -     1.89: 12
        1.89 -     2.57: 2006
        2.57 -     3.25: 6805
        3.25 -     3.92: 8024
        3.92 -     4.60: 12281
  Nonbonded interactions: 29128
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HE2 TYR A  89 "
     model   vdw
     1.213 2.450
  nonbonded model="   0" pdb=" OD1 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A  85 "
     model   vdw
     1.341 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.484 1.850
  nonbonded model="   0" pdb="HG22 ILE A  37 "
            model="   0" pdb=" HE2 PHE A  45 "
     model   vdw
     1.679 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.681 1.850
  ... (remaining 29123 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: 1.13 seconds

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


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

  Time building chain proxies: 1.21, per 1000 atoms: 0.55
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.783, 52.564, 74.355, 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.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 88
        1.23 -     1.43: 384
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.06e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.80e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.73e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.21e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.21e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.55 -   106.25: 118
      106.25 -   111.95: 2493
      111.95 -   117.65: 470
      117.65 -   123.35: 823
      123.35 -   129.05: 175
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.62    3.98 1.00e+00 1.00e+00 1.59e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.53   -3.93 1.00e+00 1.00e+00 1.55e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.96    3.64 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.07    3.53 1.00e+00 1.00e+00 1.24e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.68    4.52 1.30e+00 5.92e-01 1.21e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.63: 962
       16.63 -    33.26: 57
       33.26 -    49.89: 9
       49.89 -    66.53: 3
       66.53 -    83.16: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.46  -25.54     0      5.00e+00 4.00e-02 2.61e+01
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.39   21.61     0      5.00e+00 4.00e-02 1.87e+01
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.96  -21.04     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 78
       0.046 -    0.092: 57
       0.092 -    0.138: 31
       0.138 -    0.183: 8
       0.183 -    0.229: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 135 "
            model="   0" pdb=" N   HIS A 135 "
            model="   0" pdb=" C   HIS A 135 "
            model="   0" pdb=" CB  HIS A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.66e-01
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.39e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.085 2.00e-02 2.50e+03   3.72e-02 4.14e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.075 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.067 2.00e-02 2.50e+03   2.64e-02 2.09e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.020 2.00e-02 2.50e+03   4.13e-02 1.70e+01
        model="   0" pdb=" CG  ASP A  36 "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 340
        2.29 -     2.87: 5141
        2.87 -     3.45: 5482
        3.45 -     4.02: 7114
        4.02 -     4.60: 10580
  Nonbonded interactions: 28657
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.714 1.850
  nonbonded model="   0" pdb="HD23 LEU A 119 "
            model="   0" pdb="HD12 ILE A 122 "
     model   vdw
     1.717 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.738 1.850
  ... (remaining 28652 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: 1.05
  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.

  Histogram of bond lengths:
        0.84 -     1.03: 1113
        1.03 -     1.22: 0
        1.22 -     1.42: 463
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" NE  ARG A 129 "
       model="   0" 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="   0" pdb=" CZ  ARG A 127 "
       model="   0" 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="   0" pdb=" NE  ARG A  21 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       53.65 -    69.09: 2
       69.09 -    84.54: 0
       84.54 -    99.98: 0
       99.98 -   115.43: 2850
      115.43 -   130.87: 1239
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   53.65   55.82 3.00e+00 1.11e-01 3.46e+02
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   56.24   53.23 3.00e+00 1.11e-01 3.15e+02
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.16   -9.69 3.00e+00 1.11e-01 1.04e+01
  angle model="   0" pdb=" CA  GLY A  73 "
        model="   0" pdb=" N   GLY A  73 "
        model="   0" pdb=" H   GLY A  73 "
      ideal   model   delta    sigma   weight residual
     114.00  119.88   -5.88 3.00e+00 1.11e-01 3.84e+00
  angle model="   0" pdb=" CA  GLY A  42 "
        model="   0" pdb=" N   GLY A  42 "
        model="   0" pdb=" H   GLY A  42 "
      ideal   model   delta    sigma   weight residual
     114.00  119.88   -5.88 3.00e+00 1.11e-01 3.84e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 825
       17.86 -    35.72: 93
       35.72 -    53.58: 83
       53.58 -    71.44: 31
       71.44 -    89.29: 7
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  16 "
           model="   0" pdb=" CG  GLU A  16 "
           model="   0" pdb=" CD  GLU A  16 "
           model="   0" 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="   0" pdb=" N   GLU A   8 "
           model="   0" pdb=" CA  GLU A   8 "
           model="   0" pdb=" CB  GLU A   8 "
           model="   0" 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="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" CB  LYS A  79 "
           model="   0" pdb=" CG  LYS A  79 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" 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="   0" pdb=" CA  ILE A  38 "
            model="   0" pdb=" N   ILE A  38 "
            model="   0" pdb=" C   ILE A  38 "
            model="   0" 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="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" 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="   0" pdb=" CB  TYR A  50 "   -0.000 2.00e-02 2.50e+03   5.24e-04 8.22e-03
        model="   0" pdb=" CG  TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.000 2.00e-02 2.50e+03   4.86e-04 7.08e-03
        model="   0" pdb=" CG  TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  67 "   -0.000 2.00e-02 2.50e+03   4.59e-04 6.31e-03
        model="   0" pdb=" CG  PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  67 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  67 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  67 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  67 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  67 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.45: 1334
        2.45 -     2.99: 5201
        2.99 -     3.52: 5563
        3.52 -     4.06: 7017
        4.06 -     4.60: 9752
  Nonbonded interactions: 28867
  Sorted by model distance:
  nonbonded model="   0" pdb=" H   VAL A  14 "
            model="   0" pdb=" OE1 GLN A  66 "
     model   vdw
     1.909 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.917 1.850
  nonbonded model="   0" pdb=" O   LEU A   9 "
            model="   0" pdb=" H   SER A  13 "
     model   vdw
     1.921 1.850
  nonbonded model="   0" pdb=" O   GLU A  16 "
            model="   0" pdb=" H   THR A  20 "
     model   vdw
     1.926 1.850
  nonbonded model="   0" pdb=" O   LYS A 125 "
            model="   0" pdb=" H   ARG A 129 "
     model   vdw
     1.961 1.850
  ... (remaining 28862 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 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: "   0"
    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}

  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 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, 2224
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 60
        1.23 -     1.43: 412
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.60e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.04e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.68e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.06e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.85e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.35 -   106.08: 90
      106.08 -   111.80: 2487
      111.80 -   117.53: 485
      117.53 -   123.26: 827
      123.26 -   128.98: 190
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.38    4.22 1.00e+00 1.00e+00 1.78e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  115.99   -3.39 1.00e+00 1.00e+00 1.15e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.85    4.35 1.30e+00 5.92e-01 1.12e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.92   -3.32 1.00e+00 1.00e+00 1.10e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" 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 -    17.01: 966
       17.01 -    34.02: 50
       34.02 -    51.03: 15
       51.03 -    68.04: 1
       68.04 -    85.05: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.12  -24.88     0      5.00e+00 4.00e-02 2.48e+01
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.17  -24.83     0      5.00e+00 4.00e-02 2.47e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.79   23.21     0      5.00e+00 4.00e-02 2.16e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 79
       0.043 -    0.085: 42
       0.085 -    0.128: 40
       0.128 -    0.170: 13
       0.170 -    0.213: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.47e-01
  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    2.35    0.16 2.00e-01 2.50e+01 6.58e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.057 2.00e-02 2.50e+03   2.46e-02 1.81e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.012 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 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.054 2.00e-02 2.50e+03   2.10e-02 1.32e+01
        model="   0" pdb=" CG  TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.005 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 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.016 2.00e-02 2.50e+03   3.30e-02 1.09e+01
        model="   0" pdb=" CG  ASP A  36 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 74
        2.11 -     2.73: 3734
        2.73 -     3.35: 6224
        3.35 -     3.98: 7399
        3.98 -     4.60: 11172
  Nonbonded interactions: 28603
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  86 "
            model="   0" pdb=" H   GLY A  87 "
     model   vdw
     1.487 2.270
  nonbonded model="   0" pdb=" HE1 TYR A  81 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.547 2.100
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.618 1.850
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.693 2.440
  nonbonded model="   0" pdb=" HZ  PHE A  67 "
            model="   0" pdb=" HE1 TYR A  91 "
     model   vdw
     1.709 2.100
  ... (remaining 28598 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: 0.62
  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.


End of input processing

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

   Number of:
     all atoms      : 2224
     H or D atoms   : 1113
     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 : 1113
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1113
  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 
    0" pdbres="HIS A 134  conformer  : HE2 
    0" pdbres="HIS A 135  conformer  : HE2 
    0" pdbres="HIS A 136  conformer  : HE2 
    0" pdbres="HIS A 137  conformer  : HE2 
    0" pdbres="HIS A 138  conformer  : HE2 
    0" pdbres="HIS A 139  conformer  : HE2 

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

   A   1  MET  H2 , Angle H1-N-H2, observed: 122.733, delta from target: -13.263
   A   1  MET  H3 , Angle H1-N-H3, observed: 27.797, delta from target: 81.673

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2248  Z= 0.046
    Angle     :  1.939  81.673   4091  Z= 0.654
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 22.900  84.597    775
    Min Nonbonded Distance : 1.910
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    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   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   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 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 ===================================

  Time building chain proxies: 1.02, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.026, 46.252, 63.759, 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: (67.691, 42.828, 61.235, 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: 4
        1.23 -     1.42: 455
        1.42 -     1.61: 673
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 134 "
       model="   0" pdb=" N   HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 1.96e+00
  bond model="   0" pdb=" C   VAL A 112 "
       model="   0" pdb=" N   LYS A 113 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.91e+00
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.465  0.026 2.10e-02 2.27e+03 1.58e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.30e+00
  bond model="   0" pdb=" C   THR A  20 "
       model="   0" pdb=" N   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.28e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.76 -   106.81: 53
      106.81 -   112.87: 2721
      112.87 -   118.92: 435
      118.92 -   124.98: 830
      124.98 -   131.03: 40
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  123.62   -5.62 3.00e+00 1.11e-01 3.51e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.87   -4.87 3.00e+00 1.11e-01 2.63e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.71   -4.71 3.00e+00 1.11e-01 2.46e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  104.31    4.69 3.00e+00 1.11e-01 2.44e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.67   -4.67 3.00e+00 1.11e-01 2.42e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 984
       17.58 -    35.15: 26
       35.15 -    52.73: 9
       52.73 -    70.30: 4
       70.30 -    87.88: 10
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
           model="   0" pdb=" CD  GLU A  55 "
           model="   0" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.88  -87.88     1      3.00e+01 1.11e-03 1.03e+01
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.59  -87.59     1      3.00e+01 1.11e-03 1.02e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.67  -86.67     1      3.00e+01 1.11e-03 1.00e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.025: 106
       0.025 -    0.050: 45
       0.050 -    0.074: 10
       0.074 -    0.098: 5
       0.098 -    0.123: 10
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  chirality model="   0" pdb=" CA  ILE A  37 "
            model="   0" pdb=" N   ILE A  37 "
            model="   0" pdb=" C   ILE A  37 "
            model="   0" pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.59e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.54e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.010 2.00e-02 2.50e+03   4.54e-03 6.18e-01
        model="   0" pdb=" CG  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.009 2.00e-02 2.50e+03   4.48e-03 6.03e-01
        model="   0" pdb=" CG  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 135 "   -0.008 2.00e-02 2.50e+03   5.47e-03 5.98e-01
        model="   0" pdb=" CG  HIS A 135 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 135 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 135 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 135 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 135 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 135 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 135 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 57
        2.08 -     2.71: 3808
        2.71 -     3.34: 5887
        3.34 -     3.97: 7343
        3.97 -     4.60: 11241
  Nonbonded interactions: 28336
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A   8 "
            model="   0" pdb="HH22 ARG A  58 "
     model   vdw
     1.454 1.850
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.645 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.681 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.726 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.784 2.270
  ... (remaining 28331 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: 0.49
  Number of scatterers: 2224
  At special positions: 0
  Unit cell: (60.443, 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    1113      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   3.65 %
                favored =  75.18 %
  Rotamer outliers      =  18.55 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0009
  RMS(angles)           =   1.94
  MolProbity score      =   2.41

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}

  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: 1.11 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: 2
        1.22 -     1.42: 461
        1.42 -     1.61: 669
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   TYR A  50 "
       model="   0" pdb=" N   ILE A  51 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.76e+00
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.467  0.024 2.10e-02 2.27e+03 1.35e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.366  0.012 1.10e-02 8.26e+03 1.13e+00
  bond model="   0" pdb=" C   GLU A 120 "
       model="   0" pdb=" N   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.329  1.343 -0.014 1.40e-02 5.10e+03 1.02e+00
  bond model="   0" pdb=" C   TYR A 111 "
       model="   0" pdb=" N   VAL A 112 "
    ideal  model  delta    sigma   weight residual
    1.329  1.316  0.013 1.40e-02 5.10e+03 8.47e-01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.86 -   106.93: 56
      106.93 -   113.00: 2722
      113.00 -   119.07: 434
      119.07 -   125.14: 825
      125.14 -   131.21: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  104.33    4.67 3.00e+00 1.11e-01 2.43e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.65   -4.65 3.00e+00 1.11e-01 2.41e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.50   -4.50 3.00e+00 1.11e-01 2.25e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  104.63    4.37 3.00e+00 1.11e-01 2.12e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.31   -4.31 3.00e+00 1.11e-01 2.06e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.96: 971
       13.96 -    27.92: 39
       27.92 -    41.88: 11
       41.88 -    55.84: 8
       55.84 -    69.80: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   HIS A 135 "
           model="   0" pdb=" CA  HIS A 135 "
           model="   0" pdb=" CB  HIS A 135 "
           model="   0" pdb=" CG  HIS A 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -129.32  -50.68     3      1.50e+01 4.44e-03 8.93e+00
  dihedral model="   0" pdb=" CB  GLU A 120 "
           model="   0" pdb=" CG  GLU A 120 "
           model="   0" pdb=" CD  GLU A 120 "
           model="   0" pdb=" OE1 GLU A 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -65.83   65.83     1      3.00e+01 1.11e-03 6.30e+00
  dihedral model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" CB  HIS A 137 "
           model="   0" pdb=" CG  HIS A 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -94.31   34.31     3      1.50e+01 4.44e-03 5.80e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 116
       0.026 -    0.051: 41
       0.051 -    0.076: 9
       0.076 -    0.102: 5
       0.102 -    0.127: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.05e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.55e-01
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.26e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.014 5.00e-02 4.00e+02   2.13e-02 7.23e-01
        model="   0" pdb=" N   PRO A   6 "   -0.037 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.011 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.012 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "   -0.012 5.00e-02 4.00e+02   1.85e-02 5.48e-01
        model="   0" pdb=" N   PRO A  54 "    0.032 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "   -0.010 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "   -0.010 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ARG A  21 "   -0.011 5.00e-02 4.00e+02   1.60e-02 4.10e-01
        model="   0" pdb=" N   PRO A  22 "    0.028 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  22 "   -0.008 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  22 "   -0.009 5.00e-02 4.00e+02
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 343
        2.30 -     2.87: 5160
        2.87 -     3.45: 5310
        3.45 -     4.02: 7254
        4.02 -     4.60: 10677
  Nonbonded interactions: 28744
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.720 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.765 1.850
  nonbonded model="   0" pdb="HD23 LEU A  53 "
            model="   0" pdb="HH11 ARG A  58 "
     model   vdw
     1.777 2.270
  nonbonded model="   0" pdb="HG23 ILE A  38 "
            model="   0" pdb=" O   HIS A  43 "
     model   vdw
     1.812 2.620
  ... (remaining 28739 not shown)

  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: (43.111, 70.39, 57.341, 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: 1.04
  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 -     1.04: 1106
        1.04 -     1.23: 106
        1.23 -     1.43: 366
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.49e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.33e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.64e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.59e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.18 -   106.70: 155
      106.70 -   112.22: 2510
      112.22 -   117.74: 413
      117.74 -   123.26: 806
      123.26 -   128.77: 195
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.38    4.22 1.00e+00 1.00e+00 1.78e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.16    5.04 1.30e+00 5.92e-01 1.50e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.56    4.64 1.30e+00 5.92e-01 1.28e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.05    3.55 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.96    4.24 1.30e+00 5.92e-01 1.06e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 968
       17.15 -    34.30: 48
       34.30 -    51.45: 11
       51.45 -    68.60: 5
       68.60 -    85.75: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.74  -30.26     0      5.00e+00 4.00e-02 3.66e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.70  -20.30     0      5.00e+00 4.00e-02 1.65e+01
  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  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 83
       0.048 -    0.096: 53
       0.096 -    0.145: 32
       0.145 -    0.193: 4
       0.193 -    0.241: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality model="   0" pdb=" CA  ASP A  88 "
            model="   0" pdb=" N   ASP A  88 "
            model="   0" pdb=" C   ASP A  88 "
            model="   0" pdb=" CB  ASP A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.76e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.060 2.00e-02 2.50e+03   2.65e-02 2.11e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.064 2.00e-02 2.50e+03   2.49e-02 1.86e+01
        model="   0" pdb=" CG  TYR A  81 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.058 2.00e-02 2.50e+03   2.28e-02 1.56e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 333
        2.30 -     2.87: 5120
        2.87 -     3.45: 5410
        3.45 -     4.02: 7125
        4.02 -     4.60: 10377
  Nonbonded interactions: 28365
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.736 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.756 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.791 1.850
  ... (remaining 28360 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:    0.019 (Z=  1.390)
  Mean delta:    0.004 (Z=  0.236)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    5.527 (Z=  2.211)
  Mean delta:    0.603 (Z=  0.298)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.004
  Max. delta:   88.231
  Mean delta:   15.056

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.141
  Mean delta:    0.040

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.016
  Mean delta:    0.003

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.019   2242  Z= 0.168
    Angle     :  1.042   5.527   4079  Z= 0.373
    Chirality :  0.040   0.141    176
    Planarity :  0.002   0.016    327
    Dihedral  : 12.814  88.231    769
    Min Nonbonded Distance : 1.497
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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: -0.46 (0.64), residues: 137
    helix:  0.31 (0.62), residues: 63
    sheet:  None (None), residues: 0
    loop : -0.81 (0.63), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.001   HIS A 134 
   PHE   0.005   0.002   PHE A  45 
   TYR   0.008   0.002   TYR A  12 
   ARG   0.005   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.001   HIS A 134 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.006   0.002   TYR A  12 
   ARG   0.002   0.001   ARG A  58 

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

   A  66  GLN
   A  28  GLN

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

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

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

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0028
  RMS(angles)           =   1.04
  MolProbity score      =   1.39

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: 0.94
  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.


  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: 1.14
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  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 -     1.03: 1113
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" NE  ARG A 127 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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="   0" pdb=" CZ  ARG A  58 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       19.18 -    41.53: 1
       41.53 -    63.87: 0
       63.87 -    86.22: 0
       86.22 -   108.56: 516
      108.56 -   130.91: 3574
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   19.18   90.29 3.00e+00 1.11e-01 9.06e+02
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   90.29   19.18 3.00e+00 1.11e-01 4.09e+01
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.16   -9.69 3.00e+00 1.11e-01 1.04e+01
  angle model="   0" pdb=" CA  GLY A 121 "
        model="   0" pdb=" N   GLY A 121 "
        model="   0" pdb=" H   GLY A 121 "
      ideal   model   delta    sigma   weight residual
     114.00  119.90   -5.90 3.00e+00 1.11e-01 3.86e+00
  angle model="   0" pdb=" CA  GLY A  80 "
        model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" H   GLY A  80 "
      ideal   model   delta    sigma   weight residual
     114.00  119.89   -5.89 3.00e+00 1.11e-01 3.85e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 822
       17.99 -    35.98: 106
       35.98 -    53.96: 72
       53.96 -    71.95: 33
       71.95 -    89.94: 6
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A   7 "
           model="   0" pdb=" CB  ASP A   7 "
           model="   0" pdb=" CG  ASP A   7 "
           model="   0" 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="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" 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="   0" pdb=" CB  GLU A  16 "
           model="   0" pdb=" CG  GLU A  16 "
           model="   0" pdb=" CD  GLU A  16 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A  37 "
            model="   0" pdb=" N   ILE A  37 "
            model="   0" pdb=" C   ILE A  37 "
            model="   0" 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="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" 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="   0" pdb=" CA  ILE A  71 "
            model="   0" pdb=" N   ILE A  71 "
            model="   0" pdb=" C   ILE A  71 "
            model="   0" 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="   0" pdb=" CB  TYR A  12 "   -0.000 2.00e-02 2.50e+03   5.76e-04 9.94e-03
        model="   0" pdb=" CG  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.001 2.00e-02 2.50e+03   5.23e-04 8.20e-03
        model="   0" pdb=" CG  TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "   -0.000 2.00e-02 2.50e+03   5.14e-04 7.94e-03
        model="   0" pdb=" CG  PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.45: 1295
        2.45 -     2.98: 5078
        2.98 -     3.52: 5392
        3.52 -     4.06: 6816
        4.06 -     4.60: 9581
  Nonbonded interactions: 28162
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ILE A 108 "
            model="   0" pdb=" H   TYR A 111 "
     model   vdw
     1.907 1.850
  nonbonded model="   0" pdb=" O   PRO A 117 "
            model="   0" pdb=" H   LEU A 119 "
     model   vdw
     1.909 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.937 1.850
  nonbonded model="   0" pdb=" HB2 PRO A 117 "
            model="   0" pdb=" H   ASP A 118 "
     model   vdw
     1.971 2.270
  nonbonded model="   0" pdb=" O   LEU A  26 "
            model="   0" pdb=" H   ILE A  30 "
     model   vdw
     1.973 1.850
  ... (remaining 28157 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: 71
        1.23 -     1.43: 401
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.21e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.72e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.60e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.53e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.50 -   106.21: 103
      106.21 -   111.91: 2508
      111.91 -   117.61: 463
      117.61 -   123.32: 826
      123.32 -   129.02: 179
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.62    3.98 1.00e+00 1.00e+00 1.58e+01
  angle model="   0" pdb=" C   TYR A  81 "
        model="   0" pdb=" N   THR A  82 "
        model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta    sigma   weight residual
     121.70  128.83   -7.13 1.80e+00 3.09e-01 1.57e+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  128.44   -6.74 1.80e+00 3.09e-01 1.40e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.89    3.71 1.00e+00 1.00e+00 1.37e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.02   -4.62 1.40e+00 5.10e-01 1.09e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 967
       17.15 -    34.30: 47
       34.30 -    51.45: 11
       51.45 -    68.60: 6
       68.60 -    85.75: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  161.88   18.12     0      5.00e+00 4.00e-02 1.31e+01
  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  163.14   16.86     0      5.00e+00 4.00e-02 1.14e+01
  dihedral model="   0" pdb=" CA  GLY A  87 "
           model="   0" pdb=" C   GLY A  87 "
           model="   0" pdb=" N   ASP A  88 "
           model="   0" pdb=" CA  ASP A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.06   15.94     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.051: 84
       0.051 -    0.101: 58
       0.101 -    0.151: 30
       0.151 -    0.201: 3
       0.201 -    0.251: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 135 "
            model="   0" pdb=" N   HIS A 135 "
            model="   0" pdb=" C   HIS A 135 "
            model="   0" pdb=" CB  HIS A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality model="   0" pdb=" CA  ASP A 118 "
            model="   0" pdb=" N   ASP A 118 "
            model="   0" pdb=" C   ASP A 118 "
            model="   0" pdb=" CB  ASP A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.30e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.12e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.070 2.00e-02 2.50e+03   2.74e-02 2.25e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLU A  32 "    0.021 2.00e-02 2.50e+03   4.26e-02 1.82e+01
        model="   0" pdb=" CD  GLU A  32 "   -0.074 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLU A  32 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" OE2 GLU A  32 "    0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.047 2.00e-02 2.50e+03   1.99e-02 1.19e+01
        model="   0" pdb=" CG  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.007 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 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.011 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 315
        2.29 -     2.86: 5117
        2.86 -     3.44: 5360
        3.44 -     4.02: 7036
        4.02 -     4.60: 10513
  Nonbonded interactions: 28341
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.707 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.744 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  49 "
            model="   0" pdb=" HZ3 LYS A 125 "
     model   vdw
     1.753 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.762 1.850
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.765 2.440
  ... (remaining 28336 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: 78
        1.23 -     1.43: 395
        1.43 -     1.62: 659
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.09e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.22e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.78e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.22e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.85e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.90 -   106.51: 131
      106.51 -   112.13: 2517
      112.13 -   117.75: 442
      117.75 -   123.37: 817
      123.37 -   128.99: 172
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   ALA A 124 "
        model="   0" pdb=" CA  ALA A 124 "
        model="   0" pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     110.40  102.44    7.96 1.50e+00 4.44e-01 2.82e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.59    4.01 1.00e+00 1.00e+00 1.60e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.49   -3.89 1.00e+00 1.00e+00 1.51e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.91    3.69 1.00e+00 1.00e+00 1.36e+01
  angle model="   0" pdb=" C   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
        model="   0" pdb=" CB  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     110.10  116.88   -6.78 1.90e+00 2.77e-01 1.27e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 968
       17.39 -    34.78: 48
       34.78 -    52.16: 14
       52.16 -    69.55: 2
       69.55 -    86.94: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  156.44   23.56     0      5.00e+00 4.00e-02 2.22e+01
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.70   21.30     0      5.00e+00 4.00e-02 1.82e+01
  dihedral model="   0" pdb=" CA  VAL A 112 "
           model="   0" pdb=" C   VAL A 112 "
           model="   0" pdb=" N   LYS A 113 "
           model="   0" pdb=" CA  LYS A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.30   17.70     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 75
       0.044 -    0.088: 58
       0.088 -    0.132: 30
       0.132 -    0.175: 11
       0.175 -    0.219: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.94e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.27e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.076 2.00e-02 2.50e+03   2.99e-02 2.68e+01
        model="   0" pdb=" CG  TYR A  89 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.067 2.00e-02 2.50e+03   2.68e-02 2.16e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.060 2.00e-02 2.50e+03   2.66e-02 2.13e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        0.94 -     1.67: 2
        1.67 -     2.41: 1016
        2.41 -     3.14: 6824
        3.14 -     3.87: 8227
        3.87 -     4.60: 12894
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 28963
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 LEU A 119 "
            model="   0" pdb=" HB1 ALA A 124 "
     model   vdw
     0.944 2.440
  nonbonded model="   0" pdb=" H   GLY A  87 "
            model="   0" pdb=" HE2 TYR A  89 "
     model   vdw
     1.611 2.100
  nonbonded model="   0" pdb="HD21 ASN A  72 "
            model="   0" pdb=" HZ3 LYS A  85 "
     model   vdw
     1.687 2.100
  nonbonded model="   0" pdb=" HB2 PRO A 117 "
            model="   0" pdb=" HG  LEU A 119 "
     model   vdw
     1.709 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.733 1.850
  ... (remaining 28958 not shown)

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

============================== 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 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: "   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: 0.82
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.95 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   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    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 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: "   0"
    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: 59
        1.23 -     1.43: 413
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.31e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.81e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.77e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.50e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.43e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.55 -   106.29: 123
      106.29 -   112.03: 2496
      112.03 -   117.76: 462
      117.76 -   123.50: 846
      123.50 -   129.24: 152
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.43    4.17 1.00e+00 1.00e+00 1.74e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.03    3.57 1.00e+00 1.00e+00 1.27e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.68    4.52 1.30e+00 5.92e-01 1.21e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.05   -3.45 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.06   -4.66 1.40e+00 5.10e-01 1.11e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 964
       17.39 -    34.78: 49
       34.78 -    52.17: 16
       52.17 -    69.57: 2
       69.57 -    86.96: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.42  -34.58     0      5.00e+00 4.00e-02 4.78e+01
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.82  -24.18     0      5.00e+00 4.00e-02 2.34e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.95   19.05     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 83
       0.053 -    0.105: 57
       0.105 -    0.158: 32
       0.158 -    0.211: 3
       0.211 -    0.263: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.04e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.89e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.068 2.00e-02 2.50e+03   2.98e-02 2.66e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.057 2.00e-02 2.50e+03   2.24e-02 1.50e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.050 2.00e-02 2.50e+03   1.92e-02 1.10e+01
        model="   0" pdb=" CG  TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 78
        2.12 -     2.74: 3818
        2.74 -     3.36: 6049
        3.36 -     3.98: 7345
        3.98 -     4.60: 11141
  Nonbonded interactions: 28431
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE2 LYS A  79 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.497 2.270
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.617 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.635 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.696 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  49 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.722 1.850
  ... (remaining 28426 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:    0.040 (Z=  2.480)
  Mean delta:    0.012 (Z=  0.608)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   130.51    -8.81  1.80e+00  2.40e+01   4.9*sigma
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   130.11    -8.41  1.80e+00  2.18e+01   4.7*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:    0.001 (Z=  0.000)
  Max. delta:    8.813 (Z=  4.896)
  Mean delta:    1.701 (Z=  0.923)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   87.148
  Mean delta:   12.110

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.229
  Mean delta:    0.079

                       ----------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            0.069       0.125       96.59   6.3*sigma

  Min. delta:    0.000
  Max. delta:    0.069
  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----------                   

    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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.433
    Angle     :  1.602   8.813   4079  Z= 0.696
    Chirality :  0.079   0.229    176
    Planarity :  0.009   0.066    327
    Dihedral  : 10.910  87.148    769
    Min Nonbonded Distance : 1.565
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  6.57 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  5.65 %
      Favored  : 93.55 %
    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:  0.00 (0.71), residues: 137
    helix:  0.21 (0.50), residues: 92
    sheet:  None (None), residues: 0
    loop : -0.14 (1.07), residues: 45
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.020   0.004   PHE A  45 
   TYR   0.154   0.019   TYR A  81 
   ARG   0.035   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.013   0.004   PHE A  45 
   TYR   0.125   0.023   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 =   0.73 %
                favored =  92.70 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.60
  MolProbity score      =   1.83

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}
        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 ==============================

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.377, 40.196, 53, 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      : 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=  2.653)
  Mean delta:    0.012 (Z=  0.609)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.171 (Z=  3.900)
  Mean delta:    1.586 (Z=  0.873)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.016
  Max. delta:   86.276
  Mean delta:   13.285

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.209
  Mean delta:    0.074

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.434
    Angle     :  1.535   7.708   4079  Z= 0.666
    Chirality :  0.074   0.209    176
    Planarity :  0.008   0.037    327
    Dihedral  : 12.068  86.276    769
    Min Nonbonded Distance : 1.621
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  4.03 %
      Favored  : 92.74 %
    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:  0.50 (0.69), residues: 137
    helix:  0.45 (0.49), residues: 90
    sheet:  None (None), residues: 0
    loop :  0.40 (1.04), residues: 47
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.010   0.003   PHE A  45 
   TYR   0.084   0.012   TYR A  50 
   ARG   0.039   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.008   0.002   PHE A  67 
   TYR   0.069   0.015   TYR A  50 
   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      : 2224
     H or D atoms   : 1113
     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 : 1113
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1113
  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 
    0" pdbres="HIS A 134  conformer  : HE2 
    0" pdbres="HIS A 135  conformer  : HE2 
    0" pdbres="HIS A 136  conformer  : HE2 
    0" pdbres="HIS A 137  conformer  : HE2 
    0" pdbres="HIS A 138  conformer  : HE2 
    0" pdbres="HIS A 139  conformer  : HE2 

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

   A   1  MET  H3 , Angle H1-N-H3, observed: 131.230, delta from target: -21.760
   A   1  MET  H2 , Angle H1-N-H2, observed: 57.808, delta from target: 51.662

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2248  Z= 0.045
    Angle     :  1.690  51.662   4091  Z= 0.572
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 22.747  88.153    775
    Min Nonbonded Distance : 1.906
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    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   0.001   0.000   TYR A  12 
   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 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 ===================================

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.78, 45.945, 53.892, 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 =  97.08 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.54
  MolProbity score      =   1.70

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   4.38 %
                favored =  76.64 %
  Rotamer outliers      =  25.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0009
  RMS(angles)           =   1.69
  MolProbity score      =   2.35

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:    0.040 (Z=  2.489)
  Mean delta:    0.012 (Z=  0.623)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   129.09    -7.39  1.80e+00  1.68e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.388 (Z=  4.198)
  Mean delta:    1.601 (Z=  0.873)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.021
  Max. delta:   85.226
  Mean delta:   11.962

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.200
  Mean delta:    0.074

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.078
  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----------                   

    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 

============================ 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= 0.444
    Angle     :  1.537   7.388   4079  Z= 0.665
    Chirality :  0.074   0.200    176
    Planarity :  0.008   0.058    327
    Dihedral  : 10.893  85.226    769
    Min Nonbonded Distance : 1.663
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  4.38 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  2.42 %
      Favored  : 95.97 %
    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:  0.44 (0.70), residues: 137
    helix:  0.38 (0.51), residues: 83
    sheet:  None (None), residues: 0
    loop :  0.43 (0.96), residues: 54
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.001   HIS A 139 
   PHE   0.016   0.004   PHE A  45 
   TYR   0.063   0.011   TYR A  50 
   ARG   0.063   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.001   HIS A 139 
   PHE   0.010   0.003   PHE A  45 
   TYR   0.052   0.013   TYR A  50 
   ARG   0.007   0.002   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:    0.039 (Z=  3.054)
  Mean delta:    0.012 (Z=  0.610)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 135  HIS  CA
   A 135  HIS  CB
   A 135  HIS  CG        113.80   109.72     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   118.55     4.05  1.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:    6.054 (Z=  4.082)
  Mean delta:    1.600 (Z=  0.874)

                      ----------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   154.25    25.75  5.00e+00  2.65e+01   5.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   155.83    24.17  5.00e+00  2.34e+01   4.8*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   156.13    23.87  5.00e+00  2.28e+01   4.8*sigma

  Min. delta:    0.019
  Max. delta:   86.027
  Mean delta:   12.121

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.191
  Mean delta:    0.073

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.035
  Mean delta:    0.009

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.434
    Angle     :  1.544   6.054   4079  Z= 0.667
    Chirality :  0.073   0.191    176
    Planarity :  0.007   0.030    327
    Dihedral  : 10.819  86.027    769
    Min Nonbonded Distance : 1.339
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  1.61 %
      Favored  : 98.39 %
    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:  0.16 (0.72), residues: 137
    helix:  0.24 (0.52), residues: 82
    sheet:  None (None), residues: 0
    loop :  0.14 (0.97), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 135 
   PHE   0.015   0.004   PHE A  67 
   TYR   0.071   0.012   TYR A  50 
   ARG   0.030   0.006   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 135 
   PHE   0.008   0.003   PHE A  67 
   TYR   0.057   0.014   TYR A  50 
   ARG   0.006   0.001   ARG A  58 

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

   A 135  HIS

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

  Ramachandran outliers =   1.46 %
                favored =  94.16 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.54
  MolProbity score      =   1.87

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.54
  MolProbity score      =   1.79

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:    0.039 (Z=  3.169)
  Mean delta:    0.012 (Z=  0.617)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   117.14    -4.54  1.00e+00  2.06e+01   4.5*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

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.123 (Z=  4.544)
  Mean delta:    1.613 (Z=  0.877)

                      ----------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   152.20    27.80  5.00e+00  3.09e+01   5.6*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   154.40    25.60  5.00e+00  2.62e+01   5.1*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   155.00    25.00  5.00e+00  2.50e+01   5.0*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   155.98    24.02  5.00e+00  2.31e+01   4.8*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   156.16    23.84  5.00e+00  2.27e+01   4.8*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   156.16    23.84  5.00e+00  2.27e+01   4.8*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   157.12    22.88  5.00e+00  2.09e+01   4.6*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   157.89    22.11  5.00e+00  1.96e+01   4.4*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   157.98    22.02  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   158.88    21.12  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  -159.91   -20.09  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.002
  Max. delta:   83.247
  Mean delta:   12.109

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.233
  Mean delta:    0.073

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.109
  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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.440
    Angle     :  1.545   6.123   4079  Z= 0.668
    Chirality :  0.073   0.233    176
    Planarity :  0.009   0.083    327
    Dihedral  : 10.498  83.247    769
    Min Nonbonded Distance : 1.555
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  6.57 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  0.00 %
      Favored  : 97.58 %
    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: -1.09 (0.67), residues: 137
    helix: -0.60 (0.49), residues: 73
    sheet:  None (None), residues: 0
    loop : -0.71 (0.86), residues: 64
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.013   0.003   PHE A  45 
   TYR   0.063   0.010   TYR A  50 
   ARG   0.087   0.015   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.009   0.003   PHE A  67 
   TYR   0.052   0.011   TYR A 111 
   ARG   0.006   0.002   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      : 2224
     H or D atoms   : 1113
     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 : 1113
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1113
  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 
    0" pdbres="HIS A 134  conformer  : HE2 
    0" pdbres="HIS A 135  conformer  : HE2 
    0" pdbres="HIS A 136  conformer  : HE2 
    0" pdbres="HIS A 137  conformer  : HE2 
    0" pdbres="HIS A 138  conformer  : HE2 
    0" pdbres="HIS A 139  conformer  : HE2 

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

   A   1  MET  H3 , Angle H1-N-H3, observed: 130.025, delta from target: -20.555
   A   1  MET  H2 , Angle H1-N-H2, observed: 65.086, delta from target: 44.384

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2248  Z= 0.046
    Angle     :  1.634  44.384   4091  Z= 0.554
    Chirality :  0.035   0.097    176
    Planarity :  0.000   0.001    326
    Dihedral  : 23.464  88.652    775
    Min Nonbonded Distance : 1.912
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    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   0.001   0.000   PHE A  15 
   TYR   0.001   0.000   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 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 ===================================

  Ramachandran outliers =   3.65 %
                favored =  89.78 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.54
  MolProbity score      =   2.19

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   4.38 %
                favored =  75.91 %
  Rotamer outliers      =  18.55 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0009
  RMS(angles)           =   1.63
  MolProbity score      =   2.41

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=  2.766)
  Mean delta:    0.012 (Z=  0.617)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.88     4.72  1.00e+00  2.23e+01   4.7*sigma
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   129.50    -7.80  1.80e+00  1.88e+01   4.3*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

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.803 (Z=  4.718)
  Mean delta:    1.635 (Z=  0.890)

                      ----------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   150.99    29.01  5.00e+00  3.37e+01   5.8*sigma

  Min. delta:    0.021
  Max. delta:   63.152
  Mean delta:   11.355

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.238
  Mean delta:    0.079

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  36  ASP  CB
   A  36  ASP  CG
   A  36  ASP  OD1
   A  36  ASP  OD2           0.049       0.084       23.58   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.049
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.440
    Angle     :  1.557   7.803   4079  Z= 0.675
    Chirality :  0.079   0.238    176
    Planarity :  0.008   0.049    327
    Dihedral  : 10.546  63.152    769
    Min Nonbonded Distance : 1.547
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  5.11 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  1.61 %
      Favored  : 96.77 %
    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:  0.17 (0.71), residues: 137
    helix:  0.61 (0.51), residues: 82
    sheet: -3.38 (1.13), residues: 10
    loop :  0.35 (1.11), residues: 45
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.019   0.004   PHE A  45 
   TYR   0.082   0.008   TYR A 111 
   ARG   0.034   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.012   0.004   PHE A  45 
   TYR   0.068   0.009   TYR A 111 
   ARG   0.004   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----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.025 (Z=  1.775)
  Mean delta:    0.004 (Z=  0.282)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    5.029 (Z=  1.676)
  Mean delta:    0.654 (Z=  0.319)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   74.350
  Mean delta:   10.399

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.134
  Mean delta:    0.034

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.025
  Mean delta:    0.003

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.025   2242  Z= 0.201
    Angle     :  1.050   5.030   4079  Z= 0.378
    Chirality :  0.034   0.134    176
    Planarity :  0.002   0.025    327
    Dihedral  :  9.614  74.350    769
    Min Nonbonded Distance : 1.717
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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: -0.25 (0.65), residues: 137
    helix: -0.78 (0.54), residues: 74
    sheet: -0.57 (1.60), residues: 10
    loop :  1.29 (0.78), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.005   0.001   PHE A  45 
   TYR   0.008   0.002   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.007   0.002   TYR A 111 
   ARG   0.002   0.000   ARG A  58 

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

   A  28  GLN

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

  Ramachandran outliers =   1.46 %
                favored =  93.43 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.56
  MolProbity score      =   1.85

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   3.16
  RMS(bonds)            =   0.0032
  RMS(angles)           =   1.05
  MolProbity score      =   1.11

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   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: "   0"
    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: 1.02
  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.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 119
        1.23 -     1.43: 353
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.89e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.61e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.69e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.97e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    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:
      101.22 -   106.75: 165
      106.75 -   112.28: 2506
      112.28 -   117.81: 421
      117.81 -   123.34: 807
      123.34 -   128.87: 180
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.47    4.13 1.00e+00 1.00e+00 1.70e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.50    4.70 1.30e+00 5.92e-01 1.31e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.03    3.57 1.00e+00 1.00e+00 1.28e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.08   -3.48 1.00e+00 1.00e+00 1.21e+01
  angle model="   0" pdb=" C   ILE A  86 "
        model="   0" pdb=" N   GLY A  87 "
        model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta    sigma   weight residual
     121.70  127.93   -6.23 1.80e+00 3.09e-01 1.20e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 971
       17.18 -    34.35: 47
       34.35 -    51.53: 13
       51.53 -    68.70: 1
       68.70 -    85.88: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.35   27.65     0      5.00e+00 4.00e-02 3.06e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.51  -27.49     0      5.00e+00 4.00e-02 3.02e+01
  dihedral model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" C   HIS A 137 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.62   26.38     0      5.00e+00 4.00e-02 2.78e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 78
       0.042 -    0.083: 46
       0.083 -    0.124: 34
       0.124 -    0.165: 15
       0.165 -    0.206: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 134 "
            model="   0" pdb=" N   HIS A 134 "
            model="   0" pdb=" C   HIS A 134 "
            model="   0" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality model="   0" pdb=" CA  THR A  83 "
            model="   0" pdb=" N   THR A  83 "
            model="   0" pdb=" C   THR A  83 "
            model="   0" pdb=" CB  THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.21e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.160 2.00e-02 2.50e+03   6.55e-02 1.29e+02
        model="   0" pdb=" CG  TYR A  89 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.117 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.067 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 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.072 2.00e-02 2.50e+03   3.09e-02 2.87e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.062 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.063 2.00e-02 2.50e+03   2.49e-02 1.86e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 149
        2.19 -     2.79: 4308
        2.79 -     3.39: 6071
        3.39 -     4.00: 7242
        4.00 -     4.60: 11009
  Nonbonded interactions: 28779
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.587 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.737 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.744 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.758 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.777 1.850
  ... (remaining 28774 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      : 2224
     H or D atoms   : 1113
     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 : 1113
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1113
  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 
    0" pdbres="HIS A 134  conformer  : HE2 
    0" pdbres="HIS A 135  conformer  : HE2 
    0" pdbres="HIS A 136  conformer  : HE2 
    0" pdbres="HIS A 137  conformer  : HE2 
    0" pdbres="HIS A 138  conformer  : HE2 
    0" pdbres="HIS A 139  conformer  : HE2 

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

   A   1  MET  H2 , Angle H1-N-H2, observed: 123.286, delta from target: -13.816
   A   1  MET  H3 , Angle H1-N-H3, observed: 80.780, delta from target: 28.690

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2248  Z= 0.046
    Angle     :  1.527  28.690   4091  Z= 0.519
    Chirality :  0.035   0.095    176
    Planarity :  0.000   0.001    326
    Dihedral  : 23.136  87.874    775
    Min Nonbonded Distance : 1.913
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    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   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   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 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 ===================================


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=  2.603)
  Mean delta:    0.012 (Z=  0.609)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.334 (Z=  3.727)
  Mean delta:    1.589 (Z=  0.861)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.004
  Max. delta:   87.394
  Mean delta:   11.546

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.268
  Mean delta:    0.079

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.049
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.037   2242  Z= 0.434
    Angle     :  1.536   6.645   4079  Z= 0.661
    Chirality :  0.079   0.268    176
    Planarity :  0.008   0.039    327
    Dihedral  : 10.669  87.394    769
    Min Nonbonded Distance : 1.689
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.81 %
      Favored  : 98.39 %
    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:  0.25 (0.73), residues: 137
    helix:  0.26 (0.51), residues: 81
    sheet: -4.66 (1.13), residues: 10
    loop :  1.65 (1.10), residues: 46
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.042   0.007   PHE A  67 
   TYR   0.058   0.009   TYR A  12 
   ARG   0.042   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.024   0.007   PHE A  67 
   TYR   0.048   0.011   TYR A  12 
   ARG   0.004   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: 0.98
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.11 seconds

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

  Ramachandran outliers =   6.57 %
                favored =  76.64 %
  Rotamer outliers      =  16.94 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0009
  RMS(angles)           =   1.53
  MolProbity score      =   2.21

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.54
  MolProbity score      =   1.39

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: 3
        1.23 -     1.42: 462
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.40e-02 5.10e+03 2.99e+00
  bond model="   0" pdb=" C   GLY A  94 "
       model="   0" pdb=" N   ASP A  95 "
    ideal  model  delta    sigma   weight residual
    1.329  1.350 -0.021 1.40e-02 5.10e+03 2.32e+00
  bond model="   0" pdb=" C   ILE A  51 "
       model="   0" pdb=" N   PRO A  52 "
    ideal  model  delta    sigma   weight residual
    1.341  1.364 -0.023 1.60e-02 3.91e+03 2.02e+00
  bond model="   0" pdb=" C   MET A   1 "
       model="   0" pdb=" N   LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.65e+00
  bond model="   0" pdb=" C   LEU A  25 "
       model="   0" pdb=" N   LEU A  26 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.65e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.01 -   106.98: 124
      106.98 -   112.96: 2626
      112.96 -   118.94: 449
      118.94 -   124.92: 835
      124.92 -   130.89: 45
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.74    5.26 3.00e+00 1.11e-01 3.08e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.91    5.09 3.00e+00 1.11e-01 2.88e+00
  angle model="   0" pdb=" N   VAL A  41 "
        model="   0" pdb=" CA  VAL A  41 "
        model="   0" pdb=" HA  VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.00  104.91    5.09 3.00e+00 1.11e-01 2.88e+00
  angle model="   0" pdb=" CB  LYS A 101 "
        model="   0" pdb=" CG  LYS A 101 "
        model="   0" pdb=" CD  LYS A 101 "
      ideal   model   delta    sigma   weight residual
     111.30  107.58    3.72 2.30e+00 1.89e-01 2.61e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" 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 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 992
       17.95 -    35.90: 25
       35.90 -    53.85: 11
       53.85 -    71.80: 3
       71.80 -    89.75: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.75   89.75     1      3.00e+01 1.11e-03 1.06e+01
  dihedral model="   0" pdb=" CA  ASP A  74 "
           model="   0" pdb=" CB  ASP A  74 "
           model="   0" pdb=" CG  ASP A  74 "
           model="   0" pdb=" OD1 ASP A  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.86   54.86     1      2.00e+01 2.50e-03 1.02e+01
  dihedral model="   0" pdb=" CA  GLU A 133 "
           model="   0" pdb=" C   GLU A 133 "
           model="   0" pdb=" N   HIS A 134 "
           model="   0" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -168.09  -11.91     0      5.00e+00 4.00e-02 5.67e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.029: 86
       0.029 -    0.057: 60
       0.057 -    0.085: 21
       0.085 -    0.113: 6
       0.113 -    0.142: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 5.01e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.43e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.019 2.00e-02 2.50e+03   7.57e-03 1.72e+00
        model="   0" pdb=" CG  TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.017 2.00e-02 2.50e+03   6.99e-03 1.47e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.005 2.00e-02 2.50e+03   1.09e-02 1.19e+00
        model="   0" pdb=" CG  ASP A  36 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 188
        2.23 -     2.82: 4781
        2.82 -     3.42: 5824
        3.42 -     4.01: 7628
        4.01 -     4.60: 11426
  Nonbonded interactions: 29847
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.641 1.850
  nonbonded model="   0" pdb=" HB3 HIS A 137 "
            model="   0" pdb=" HD2 HIS A 139 "
     model   vdw
     1.646 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.664 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  29 "
            model="   0" pdb="HD22 ASN A  72 "
     model   vdw
     1.763 1.850
  nonbonded model="   0" pdb=" O   VAL A  41 "
            model="   0" pdb=" H   LYS A 113 "
     model   vdw
     1.770 1.850
  ... (remaining 29842 not shown)

  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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== 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:    0.040 (Z=  2.715)
  Mean delta:    0.012 (Z=  0.597)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    7.680 (Z=  3.987)
  Mean delta:    1.597 (Z=  0.878)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   143.12    36.88  5.00e+00  5.44e+01   7.4*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -158.83   -21.17  5.00e+00  1.79e+01   4.2*sigma

  Min. delta:    0.000
  Max. delta:   84.010
  Mean delta:   10.460

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.195
  Mean delta:    0.072

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.046
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.425
    Angle     :  1.533   7.680   4079  Z= 0.667
    Chirality :  0.072   0.195    176
    Planarity :  0.008   0.038    327
    Dihedral  :  9.875  84.010    769
    Min Nonbonded Distance : 1.006
  
  Molprobity Statistics.
    All-atom Clashscore : 10.82
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  1.46 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  1.61 %
      Favored  : 98.39 %
    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:  0.71 (0.70), residues: 137
    helix:  0.42 (0.53), residues: 86
    sheet:  None (None), residues: 0
    loop :  0.89 (0.93), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 136 
   PHE   0.018   0.004   PHE A  45 
   TYR   0.090   0.014   TYR A  81 
   ARG   0.040   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 136 
   PHE   0.012   0.004   PHE A  45 
   TYR   0.072   0.017   TYR A  81 
   ARG   0.004   0.001   ARG A 129 

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

   A 135  HIS
   A 139  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:    0.038 (Z=  2.674)
  Mean delta:    0.011 (Z=  0.592)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.765 (Z=  3.940)
  Mean delta:    1.583 (Z=  0.864)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00  -152.27   -27.73  5.00e+00  3.08e+01   5.5*sigma

  Min. delta:    0.005
  Max. delta:   89.109
  Mean delta:   11.803

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.227
  Mean delta:    0.080

                       ----------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            0.120       0.223      286.56  11.2*sigma

  Min. delta:    0.000
  Max. delta:    0.120
  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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.421
    Angle     :  1.531   6.765   4079  Z= 0.661
    Chirality :  0.080   0.227    176
    Planarity :  0.010   0.111    327
    Dihedral  : 10.592  89.109    769
    Min Nonbonded Distance : 1.721
  
  Molprobity Statistics.
    All-atom Clashscore : 9.92
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  0.73 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  2.42 %
      Favored  : 97.58 %
    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: -0.61 (0.64), residues: 137
    helix:  0.07 (0.48), residues: 94
    sheet: -3.23 (0.93), residues: 10
    loop : -0.35 (1.00), residues: 33
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS A 139 
   PHE   0.040   0.007   PHE A  67 
   TYR   0.272   0.019   TYR A  81 
   ARG   0.039   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS A 139 
   PHE   0.024   0.007   PHE A  67 
   TYR   0.223   0.023   TYR A  81 
   ARG   0.005   0.001   ARG A  21 

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

   A  43  HIS

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


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


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


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

  Ramachandran outliers =   1.46 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  10.82
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.53
  MolProbity score      =   1.72

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  98.54 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   9.92
  RMS(bonds)            =   0.0081
  RMS(angles)           =   1.53
  MolProbity score      =   1.52

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.232, 56.754, 56.977, 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      : 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:    0.026 (Z=  1.626)
  Mean delta:    0.004 (Z=  0.272)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.525 (Z=  1.422)
  Mean delta:    0.747 (Z=  0.360)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   83.419
  Mean delta:    9.945

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.142
  Mean delta:    0.038

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.020
  Mean delta:    0.003

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.026   2242  Z= 0.194
    Angle     :  1.086   5.037   4079  Z= 0.396
    Chirality :  0.038   0.142    176
    Planarity :  0.002   0.020    327
    Dihedral  :  9.234  83.419    769
    Min Nonbonded Distance : 1.776
  
  Molprobity Statistics.
    All-atom Clashscore : 2.25
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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:  0.05 (0.64), residues: 137
    helix: -0.15 (0.58), residues: 69
    sheet:  None (None), residues: 0
    loop :  0.46 (0.66), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.005   0.002   PHE A  45 
   TYR   0.009   0.002   TYR A 111 
   ARG   0.006   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.009   0.002   TYR A 111 
   ARG   0.002   0.000   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


  Symmetric amino acids flipped
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "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: "   0"
    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:    0.038 (Z=  2.946)
  Mean delta:    0.012 (Z=  0.611)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.55     4.05  1.00e+00  1.64e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.830 (Z=  4.050)
  Mean delta:    1.564 (Z=  0.847)

                      ----------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   155.50    24.50  5.00e+00  2.40e+01   4.9*sigma

  Min. delta:    0.015
  Max. delta:   84.654
  Mean delta:   12.547

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.194
  Mean delta:    0.073

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.053
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.435
    Angle     :  1.521   6.830   4079  Z= 0.652
    Chirality :  0.073   0.194    176
    Planarity :  0.008   0.040    327
    Dihedral  : 11.363  88.559    769
    Min Nonbonded Distance : 1.639
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.03 %
      Favored  : 93.55 %
    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:  0.56 (0.70), residues: 137
    helix:  0.55 (0.51), residues: 83
    sheet:  None (None), residues: 0
    loop :  0.33 (0.94), residues: 54
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.018   0.005   PHE A  45 
   TYR   0.066   0.010   TYR A 111 
   ARG   0.043   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.011   0.004   PHE A  45 
   TYR   0.055   0.012   TYR A 111 
   ARG   0.005   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   2.25
  RMS(bonds)            =   0.0032
  RMS(angles)           =   1.09
  MolProbity score      =   1.00

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:    0.038 (Z=  2.516)
  Mean delta:    0.012 (Z=  0.616)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    7.317 (Z=  4.219)
  Mean delta:    1.608 (Z=  0.876)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   87.311
  Mean delta:   11.424

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.205
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.055
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.439
    Angle     :  1.541   7.317   4079  Z= 0.667
    Chirality :  0.076   0.205    176
    Planarity :  0.008   0.041    327
    Dihedral  : 10.005  87.311    769
    Min Nonbonded Distance : 1.589
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  2.42 %
      Favored  : 96.77 %
    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:  0.34 (0.72), residues: 137
    helix:  0.33 (0.52), residues: 77
    sheet:  None (None), residues: 0
    loop :  0.31 (0.95), residues: 60
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 136 
   PHE   0.036   0.007   PHE A  67 
   TYR   0.067   0.011   TYR A  12 
   ARG   0.041   0.011   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 136 
   PHE   0.022   0.006   PHE A  67 
   TYR   0.056   0.013   TYR A 111 
   ARG   0.005   0.002   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.52
  MolProbity score      =   1.97

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 =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   4.51
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.54
  MolProbity score      =   1.53

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:    0.040 (Z=  2.343)
  Mean delta:    0.012 (Z=  0.605)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.082 (Z=  3.911)
  Mean delta:    1.621 (Z=  0.873)

                      ----------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   143.78    36.22  5.00e+00  5.25e+01   7.2*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   153.08    26.92  5.00e+00  2.90e+01   5.4*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   155.46    24.54  5.00e+00  2.41e+01   4.9*sigma

  Min. delta:    0.062
  Max. delta:   87.099
  Mean delta:   13.186

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.197
  Mean delta:    0.073

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.054
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.431
    Angle     :  1.549   7.082   4079  Z= 0.666
    Chirality :  0.073   0.197    176
    Planarity :  0.008   0.054    327
    Dihedral  : 11.805  87.099    769
    Min Nonbonded Distance : 1.532
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  2.92 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  1.61 %
      Favored  : 96.77 %
    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: -0.70 (0.69), residues: 137
    helix: -0.22 (0.50), residues: 83
    sheet: -4.03 (0.77), residues: 10
    loop :  0.42 (1.08), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.016   0.003   PHE A  45 
   TYR   0.057   0.010   TYR A 111 
   ARG   0.036   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.010   0.003   PHE A  45 
   TYR   0.048   0.012   TYR A 111 
   ARG   0.006   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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

  Ramachandran outliers =   3.65 %
                favored =  93.43 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.55
  MolProbity score      =   2.03

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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== 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:    0.054 (Z=  2.845)
  Mean delta:    0.012 (Z=  0.617)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  32  GLU  CB
   A  32  GLU  CG
   A  32  GLU  CD        112.60   119.46    -6.86  1.70e+00  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.204 (Z=  4.038)
  Mean delta:    1.632 (Z=  0.878)

                      ----------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  -158.73   -21.27  5.00e+00  1.81e+01   4.3*sigma

  Min. delta:    0.014
  Max. delta:   86.653
  Mean delta:   11.908

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.199
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.083
  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----------                   

    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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.054   2242  Z= 0.439
    Angle     :  1.555   7.204   4079  Z= 0.669
    Chirality :  0.076   0.199    176
    Planarity :  0.009   0.062    327
    Dihedral  : 10.433  86.653    769
    Min Nonbonded Distance : 0.878
  
  Molprobity Statistics.
    All-atom Clashscore : 9.92
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  1.61 %
      Favored  : 96.77 %
    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:  0.44 (0.69), residues: 137
    helix:  0.47 (0.51), residues: 85
    sheet:  None (None), residues: 0
    loop :  0.23 (0.92), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.012   0.003   PHE A  45 
   TYR   0.068   0.013   TYR A 111 
   ARG   0.067   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.010   0.003   PHE A  67 
   TYR   0.057   0.015   TYR A 111 
   ARG   0.007   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.659, 64.949, 44.579, 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      : 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=  2.462)
  Mean delta:    0.011 (Z=  0.592)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.070 (Z=  3.985)
  Mean delta:    1.615 (Z=  0.875)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00  -154.46   -25.54  5.00e+00  2.61e+01   5.1*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   158.39    21.61  5.00e+00  1.87e+01   4.3*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -158.96   -21.04  5.00e+00  1.77e+01   4.2*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   159.76    20.24  5.00e+00  1.64e+01   4.0*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   159.96    20.04  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.002
  Max. delta:   83.156
  Mean delta:   11.452

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.229
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.042
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.421
    Angle     :  1.551   7.070   4079  Z= 0.669
    Chirality :  0.076   0.229    176
    Planarity :  0.008   0.041    327
    Dihedral  : 10.764  83.156    769
    Min Nonbonded Distance : 1.714
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  5.11 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  1.61 %
      Favored  : 97.58 %
    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: -0.18 (0.70), residues: 137
    helix:  0.29 (0.54), residues: 75
    sheet: -3.31 (0.93), residues: 10
    loop :  0.24 (0.97), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.019   0.004   PHE A  45 
   TYR   0.085   0.012   TYR A  50 
   ARG   0.034   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.012   0.003   PHE A  45 
   TYR   0.069   0.014   TYR A  50 
   ARG   0.005   0.001   ARG A  21 

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

   A  66  GLN

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

  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   9.92
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.55
  MolProbity score      =   1.98

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----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.928)
  Mean delta:    0.011 (Z=  0.593)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.205 (Z=  3.889)
  Mean delta:    1.542 (Z=  0.842)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.058
  Max. delta:   84.514
  Mean delta:   11.381

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.225
  Mean delta:    0.074

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.048
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.422
    Angle     :  1.502   6.205   4079  Z= 0.647
    Chirality :  0.074   0.225    176
    Planarity :  0.007   0.035    327
    Dihedral  : 10.291  84.514    769
    Min Nonbonded Distance : 1.611
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  1.61 %
      Favored  : 97.58 %
    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:  0.62 (0.71), residues: 137
    helix:  0.66 (0.53), residues: 81
    sheet: -3.02 (1.10), residues: 12
    loop :  1.39 (1.07), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.021   0.004   PHE A  45 
   TYR   0.066   0.009   TYR A 111 
   ARG   0.040   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.004   PHE A  45 
   TYR   0.054   0.010   TYR A 111 
   ARG   0.006   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   1.46 %
                favored =  93.43 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0081
  RMS(angles)           =   1.55
  MolProbity score      =   1.72

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 ==============================

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0080
  RMS(angles)           =   1.50
  MolProbity score      =   1.51

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 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: "   0"
    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      : 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=  2.682)
  Mean delta:    0.011 (Z=  0.576)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.124 (Z=  3.984)
  Mean delta:    1.563 (Z=  0.854)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00  -155.49   -24.51  5.00e+00  2.40e+01   4.9*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   157.81    22.19  5.00e+00  1.97e+01   4.4*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00  -158.62   -21.38  5.00e+00  1.83e+01   4.3*sigma
   A 112  VAL  CA
   A 112  VAL  C
   A 113  LYS  N
   A 113  LYS  CA        180.00   159.72    20.28  5.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.022
  Max. delta:   85.460
  Mean delta:   12.881

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.232
  Mean delta:    0.071

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.078
  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----------                   

    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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.410
    Angle     :  1.507   6.567   4079  Z= 0.652
    Chirality :  0.071   0.232    176
    Planarity :  0.009   0.059    327
    Dihedral  : 11.308  85.460    769
    Min Nonbonded Distance : 1.616
  
  Molprobity Statistics.
    All-atom Clashscore : 10.37
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  0.81 %
      Favored  : 95.16 %
    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: -0.66 (0.67), residues: 137
    helix:  0.25 (0.51), residues: 82
    sheet: -3.09 (0.71), residues: 10
    loop : -0.86 (0.99), residues: 45
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A  43 
   PHE   0.039   0.007   PHE A  45 
   TYR   0.085   0.009   TYR A 111 
   ARG   0.063   0.015   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A  43 
   PHE   0.026   0.007   PHE A  45 
   TYR   0.070   0.011   TYR A 111 
   ARG   0.006   0.002   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:    0.039 (Z=  2.958)
  Mean delta:    0.011 (Z=  0.608)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   129.98    -8.28  1.80e+00  2.12e+01   4.6*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:    0.000 (Z=  0.000)
  Max. delta:    8.285 (Z=  4.603)
  Mean delta:    1.672 (Z=  0.903)

                      ----------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   137.07    42.93  5.00e+00  7.37e+01   8.6*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00  -149.48   -30.52  5.00e+00  3.73e+01   6.1*sigma
   A  78  ILE  CA
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        180.00   153.84    26.16  5.00e+00  2.74e+01   5.2*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00  -154.34   -25.66  5.00e+00  2.63e+01   5.1*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -157.48   -22.52  5.00e+00  2.03e+01   4.5*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   158.11    21.89  5.00e+00  1.92e+01   4.4*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   159.77    20.23  5.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.034
  Max. delta:   86.414
  Mean delta:   13.107

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.269
  Mean delta:    0.080

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.065
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.433
    Angle     :  1.591   8.285   4079  Z= 0.687
    Chirality :  0.080   0.269    176
    Planarity :  0.008   0.048    327
    Dihedral  : 11.274  86.414    769
    Min Nonbonded Distance : 1.722
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  2.19 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.84 %
      Favored  : 92.74 %
    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:  0.70 (0.75), residues: 137
    helix:  0.68 (0.53), residues: 80
    sheet: -1.89 (1.60), residues: 10
    loop :  0.99 (1.15), residues: 47
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.059   0.011   TYR A  81 
   ARG   0.053   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.010   0.004   PHE A  67 
   TYR   0.049   0.013   TYR A  81 
   ARG   0.007   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


============================== 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: 1.05
  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.

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:    0.026 (Z=  1.402)
  Mean delta:    0.004 (Z=  0.254)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    5.621 (Z=  1.874)
  Mean delta:    0.566 (Z=  0.286)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.018
  Max. delta:   87.876
  Mean delta:   15.341

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.123
  Mean delta:    0.040

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.015
  Mean delta:    0.003

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.026   2242  Z= 0.181
    Angle     :  1.031   5.621   4079  Z= 0.368
    Chirality :  0.040   0.123    176
    Planarity :  0.002   0.015    327
    Dihedral  : 12.706  87.876    769
    Min Nonbonded Distance : 1.454
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.81 %
      Favored  : 99.19 %
    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: -0.61 (0.60), residues: 137
    helix: -0.28 (0.53), residues: 70
    sheet:  None (None), residues: 0
    loop : -0.39 (0.65), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.006   0.002   PHE A  45 
   TYR   0.010   0.002   TYR A 111 
   ARG   0.005   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.005   0.002   PHE A  67 
   TYR   0.009   0.002   TYR A 111 
   ARG   0.001   0.000   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =  10.37
  RMS(bonds)            =   0.0079
  RMS(angles)           =   1.51
  MolProbity score      =   2.16

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: 94
        1.23 -     1.43: 378
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 8.80e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.29e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.45e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.26e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.16e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.35 -   107.22: 407
      107.22 -   114.09: 2518
      114.09 -   120.96: 651
      120.96 -   127.83: 499
      127.83 -   134.70: 4
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  134.70  -13.00 1.80e+00 3.09e-01 5.22e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.32    4.28 1.00e+00 1.00e+00 1.83e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  125.97    5.23 1.30e+00 5.92e-01 1.62e+01
  angle model="   0" pdb=" C   LEU A 119 "
        model="   0" pdb=" N   GLU A 120 "
        model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta    sigma   weight residual
     121.70  128.51   -6.81 1.80e+00 3.09e-01 1.43e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.29    4.91 1.30e+00 5.92e-01 1.43e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 967
       17.03 -    34.07: 46
       34.07 -    51.10: 14
       51.10 -    68.13: 5
       68.13 -    85.17: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      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="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.19  -19.81     0      5.00e+00 4.00e-02 1.57e+01
  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  161.47   18.53     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.003 -    0.047: 85
       0.047 -    0.090: 45
       0.090 -    0.134: 34
       0.134 -    0.177: 10
       0.177 -    0.221: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.93e-01
  chirality model="   0" pdb=" CA  GLU A 120 "
            model="   0" pdb=" N   GLU A 120 "
            model="   0" pdb=" C   GLU A 120 "
            model="   0" pdb=" CB  GLU A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.74e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.061 2.00e-02 2.50e+03   2.38e-02 1.70e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.053 2.00e-02 2.50e+03   2.32e-02 1.61e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.011 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 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.057 2.00e-02 2.50e+03   2.24e-02 1.50e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 197
        2.23 -     2.82: 4564
        2.82 -     3.41: 5852
        3.41 -     4.01: 7195
        4.01 -     4.60: 10770
  Nonbonded interactions: 28578
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.635 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.717 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.731 1.850
  nonbonded model="   0" pdb=" H   ILE A  86 "
            model="   0" pdb="HG13 ILE A  86 "
     model   vdw
     1.744 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.747 1.850
  ... (remaining 28573 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   2.92 %
                favored =  94.89 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.59
  MolProbity score      =   1.99

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.66
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.03
  MolProbity score      =   1.58

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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

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


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


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


End of input processing

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

   Number of:
     all atoms      : 2224
     H or D atoms   : 1113
     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 : 1113
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1113
  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 
    0" pdbres="HIS A 134  conformer  : HE2 
    0" pdbres="HIS A 135  conformer  : HE2 
    0" pdbres="HIS A 136  conformer  : HE2 
    0" pdbres="HIS A 137  conformer  : HE2 
    0" pdbres="HIS A 138  conformer  : HE2 
    0" pdbres="HIS A 139  conformer  : HE2 

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

   A   1  MET  H3 , Angle H1-N-H3, observed: 56.243, delta from target: 53.227
   A   1  MET  H2 , Angle H1-N-H2, observed: 53.649, delta from target: 55.821

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.033   2248  Z= 0.046
    Angle     :  1.881  55.821   4091  Z= 0.635
    Chirality :  0.034   0.095    176
    Planarity :  0.000   0.001    326
    Dihedral  : 22.806  89.295    775
    Min Nonbonded Distance : 1.909
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    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   0.001   0.000   PHE A  45 
   TYR   0.001   0.000   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 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 ===================================


  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  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: "   0"
    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 =   3.65 %
                favored =  78.83 %
  Rotamer outliers      =  20.16 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0009
  RMS(angles)           =   1.88
  MolProbity score      =   2.24

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:    0.037 (Z=  2.622)
  Mean delta:    0.011 (Z=  0.590)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.509 (Z=  3.865)
  Mean delta:    1.556 (Z=  0.851)

                      ----------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   158.80    21.20  5.00e+00  1.80e+01   4.2*sigma

  Min. delta:    0.009
  Max. delta:   77.716
  Mean delta:   11.358

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.274
  Mean delta:    0.077

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.078
  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----------                   

    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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.037   2242  Z= 0.420
    Angle     :  1.511   7.231   4079  Z= 0.652
    Chirality :  0.077   0.274    176
    Planarity :  0.009   0.058    327
    Dihedral  : 10.892  82.836    769
    Min Nonbonded Distance : 1.213
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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:  0.88 (0.70), residues: 137
    helix:  0.65 (0.54), residues: 82
    sheet:  None (None), residues: 0
    loop :  0.75 (0.91), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.011   0.003   PHE A  45 
   TYR   0.104   0.013   TYR A  68 
   ARG   0.063   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.007   0.003   PHE A  45 
   TYR   0.083   0.015   TYR A  68 
   ARG   0.009   0.002   ARG A 127 

                     ----------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}
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 =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.66
  RMS(bonds)            =   0.0081
  RMS(angles)           =   1.51
  MolProbity score      =   1.58

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 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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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 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: "   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: (56.865, 56.641, 68.318, 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   49": "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 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: "   0"
    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 ==============================

   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:    0.037 (Z=  2.757)
  Mean delta:    0.012 (Z=  0.620)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.686 (Z=  4.222)
  Mean delta:    1.617 (Z=  0.882)

                      ----------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  -155.12   -24.88  5.00e+00  2.48e+01   5.0*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -155.17   -24.83  5.00e+00  2.47e+01   5.0*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   156.79    23.21  5.00e+00  2.16e+01   4.6*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   158.53    21.47  5.00e+00  1.84e+01   4.3*sigma

  Min. delta:    0.033
  Max. delta:   85.052
  Mean delta:   12.218

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.213
  Mean delta:    0.077

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.042
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.037   2242  Z= 0.441
    Angle     :  1.561   6.686   4079  Z= 0.674
    Chirality :  0.077   0.213    176
    Planarity :  0.007   0.034    327
    Dihedral  : 10.768  85.052    769
    Min Nonbonded Distance : 1.487
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.92 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  3.23 %
      Favored  : 96.77 %
    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:  0.02 (0.69), residues: 137
    helix: -0.15 (0.51), residues: 72
    sheet: -2.46 (1.43), residues: 10
    loop :  1.13 (0.95), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.012   0.003   PHE A  45 
   TYR   0.057   0.010   TYR A  50 
   ARG   0.034   0.009   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.009   0.003   PHE A  67 
   TYR   0.047   0.012   TYR A  50 
   ARG   0.006   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----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.024 (Z=  1.327)
  Mean delta:    0.004 (Z=  0.209)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    3.183 (Z=  1.328)
  Mean delta:    0.621 (Z=  0.315)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.010
  Max. delta:   69.800
  Mean delta:    9.819

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.127
  Mean delta:    0.035

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.021
  Mean delta:    0.003

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.024   2242  Z= 0.149
    Angle     :  1.047   4.673   4079  Z= 0.378
    Chirality :  0.035   0.127    176
    Planarity :  0.002   0.021    327
    Dihedral  :  9.629  69.800    769
    Min Nonbonded Distance : 1.720
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.00 %
      Favored  : 99.19 %
    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: -0.41 (0.63), residues: 137
    helix: -0.52 (0.54), residues: 71
    sheet:  0.18 (1.42), residues: 12
    loop :  0.28 (0.73), residues: 54
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 137 
   PHE   0.003   0.001   PHE A  15 
   TYR   0.007   0.002   TYR A  12 
   ARG   0.004   0.001   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 137 
   PHE   0.002   0.001   PHE A  15 
   TYR   0.006   0.001   TYR A 111 
   ARG   0.002   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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== 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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.73 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.56
  MolProbity score      =   1.62

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: {'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: 1.07
  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.

        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)----------                  

  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0026
  RMS(angles)           =   1.05
  MolProbity score      =   1.37

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 465
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.28e+00
  bond model="   0" pdb=" C   ASP A 118 "
       model="   0" pdb=" N   LEU A 119 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.24e+00
  bond model="   0" pdb=" C   GLN A 100 "
       model="   0" pdb=" N   LYS A 101 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.06e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.307  0.014 1.00e-02 1.00e+04 1.99e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.334 -0.013 1.00e-02 1.00e+04 1.71e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.75 -   106.84: 87
      106.84 -   112.93: 2672
      112.93 -   119.02: 446
      119.02 -   125.11: 831
      125.11 -   131.19: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   ILE A 131 "
        model="   0" pdb=" CA  ILE A 131 "
        model="   0" pdb=" C   ILE A 131 "
      ideal   model   delta    sigma   weight residual
     111.00  104.74    6.26 2.80e+00 1.28e-01 5.00e+00
  angle model="   0" pdb=" C   PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  103.35    5.65 3.00e+00 1.11e-01 3.55e+00
  angle model="   0" pdb=" CB  PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  114.39   -5.39 3.00e+00 1.11e-01 3.22e+00
  angle model="   0" pdb=" N   VAL A  41 "
        model="   0" pdb=" CA  VAL A  41 "
        model="   0" pdb=" HA  VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.00  104.82    5.18 3.00e+00 1.11e-01 2.98e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  104.84    5.16 3.00e+00 1.11e-01 2.96e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 990
       17.81 -    35.62: 23
       35.62 -    53.42: 11
       53.42 -    71.23: 3
       71.23 -    89.04: 6
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -80.95   80.95     1      3.00e+01 1.11e-03 8.99e+00
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   78.51  -78.51     1      3.00e+01 1.11e-03 8.54e+00
  dihedral model="   0" pdb=" CB  GLU A  16 "
           model="   0" pdb=" CG  GLU A  16 "
           model="   0" pdb=" CD  GLU A  16 "
           model="   0" pdb=" OE1 GLU A  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.12   78.12     1      3.00e+01 1.11e-03 8.47e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 107
       0.043 -    0.085: 43
       0.085 -    0.128: 22
       0.128 -    0.171: 1
       0.171 -    0.213: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.09e-01
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.33e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.021 2.00e-02 2.50e+03   8.24e-03 2.04e+00
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 135 "    0.013 2.00e-02 2.50e+03   8.91e-03 1.59e+00
        model="   0" pdb=" CG  HIS A 135 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 135 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 135 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 135 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 135 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 135 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 135 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        model="   0" pdb=" N   PRO A   6 "   -0.050 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.015 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.016 5.00e-02 4.00e+02
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 36
        2.08 -     2.71: 3724
        2.71 -     3.34: 6081
        3.34 -     3.97: 7564
        3.97 -     4.60: 11528
  Nonbonded interactions: 28933
  Sorted by model distance:
  nonbonded model="   0" pdb="HG12 VAL A 112 "
            model="   0" pdb=" HD3 PRO A 114 "
     model   vdw
     1.452 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.504 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.740 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.760 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.760 1.850
  ... (remaining 28928 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 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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.65, per 1000 atoms: 0.29
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (74.054, 53.878, 43.831, 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: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.014, 74.748, 45.327, 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: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.913, 39.439, 52.718, 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.

============================== 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}
        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}

End of input processing

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

   Number of:
     all atoms      : 2224
     H or D atoms   : 1113
     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 : 1113
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1113
  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 
    0" pdbres="HIS A 134  conformer  : HE2 
    0" pdbres="HIS A 135  conformer  : HE2 
    0" pdbres="HIS A 136  conformer  : HE2 
    0" pdbres="HIS A 137  conformer  : HE2 
    0" pdbres="HIS A 138  conformer  : HE2 
    0" pdbres="HIS A 139  conformer  : HE2 

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

   A   1  MET  H2 , Angle H1-N-H2, observed: 90.290, delta from target: 19.180
   A   1  MET  H3 , Angle H1-N-H3, observed: 19.183, delta from target: 90.287

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.001   0.032   2248  Z= 0.045
    Angle     :  2.042  90.287   4091  Z= 0.688
    Chirality :  0.035   0.094    176
    Planarity :  0.000   0.001    326
    Dihedral  : 22.663  89.937    775
    Min Nonbonded Distance : 1.907
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    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   0.001   0.000   PHE A  67 
   TYR   0.001   0.000   TYR A  68 
   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 ===================================

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

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

        Number of residues, atoms: 139, 2224
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Ramachandran outliers =   5.11 %
                favored =  80.29 %
  Rotamer outliers      =  22.58 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0009
  RMS(angles)           =   2.04
  MolProbity score      =   2.26

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.85, per 1000 atoms: 0.38
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (71.764, 40.345, 43.632, 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      : 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=  2.736)
  Mean delta:    0.012 (Z=  0.638)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.797 (Z=  4.221)
  Mean delta:    1.619 (Z=  0.882)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00  -149.74   -30.26  5.00e+00  3.66e+01   6.1*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00  -159.70   -20.30  5.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.050
  Max. delta:   85.753
  Mean delta:   12.791

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.241
  Mean delta:    0.079

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.042
  Mean delta:    0.010

============================= 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 

============================ 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= 0.454
    Angle     :  1.553   6.797   4079  Z= 0.672
    Chirality :  0.079   0.241    176
    Planarity :  0.008   0.033    327
    Dihedral  : 10.940  85.753    769
    Min Nonbonded Distance : 1.723
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.84 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  2.42 %
      Favored  : 95.16 %
    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: -0.53 (0.70), residues: 137
    helix: -0.03 (0.50), residues: 81
    sheet: -2.98 (1.16), residues: 10
    loop :  0.04 (1.12), residues: 46
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.064   0.012   TYR A  81 
   ARG   0.036   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.008   0.003   PHE A  45 
   TYR   0.053   0.014   TYR A  81 
   ARG   0.005   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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


  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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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 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: "   0"
    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: (48.446, 65.751, 43.925, 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: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (40.758, 61.36, 64.524, 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 =  93.43 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   2.71
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.55
  MolProbity score      =   1.78

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.69, per 1000 atoms: 0.31
  Number of scatterers: 2224
  At special positions: 0
  Unit cell: (46.489, 57.147, 72.252, 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    1113      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: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.512, 48.775, 42.481, 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.

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


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


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


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A ASP   29": "OD1" <-> "OD2"
    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 ASP   74": "OD1" <-> "OD2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A ASP   95": "OD1" <-> "OD2"
    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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    None
  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: ""

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:    0.038 (Z=  2.511)
  Mean delta:    0.011 (Z=  0.596)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.542 (Z=  4.168)
  Mean delta:    1.629 (Z=  0.881)

                      ----------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  -145.42   -34.58  5.00e+00  4.78e+01   6.9*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -155.82   -24.18  5.00e+00  2.34e+01   4.8*sigma

  Min. delta:    0.022
  Max. delta:   86.956
  Mean delta:   12.887

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.263
  Mean delta:    0.079

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.070
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.424
    Angle     :  1.569   6.542   4079  Z= 0.675
    Chirality :  0.079   0.263    176
    Planarity :  0.008   0.052    327
    Dihedral  : 11.465  86.956    769
    Min Nonbonded Distance : 1.497
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  3.23 %
      Favored  : 93.55 %
    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:  0.32 (0.71), residues: 137
    helix:  0.46 (0.55), residues: 76
    sheet: -3.33 (1.15), residues: 12
    loop :  1.17 (0.99), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.017   0.004   PHE A  45 
   TYR   0.068   0.010   TYR A  50 
   ARG   0.057   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.011   0.004   PHE A  45 
   TYR   0.056   0.011   TYR A  50 
   ARG   0.006   0.001   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: 0.75
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.88 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=  2.663)
  Mean delta:    0.012 (Z=  0.595)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40   102.44     7.96  1.50e+00  2.82e+01   5.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.59     4.01  1.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.960 (Z=  5.307)
  Mean delta:    1.656 (Z=  0.889)

                      ----------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   156.44    23.56  5.00e+00  2.22e+01   4.7*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   158.70    21.30  5.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.029
  Max. delta:   86.940
  Mean delta:   11.936

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.219
  Mean delta:    0.075

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.034
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.424
    Angle     :  1.568   7.960   4079  Z= 0.675
    Chirality :  0.075   0.219    176
    Planarity :  0.007   0.030    327
    Dihedral  : 10.827  86.940    769
    Min Nonbonded Distance : 0.944
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  4.38 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.81 %
      Favored  : 98.39 %
    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: -0.25 (0.67), residues: 137
    helix:  0.34 (0.50), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.80 (0.88), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.001   HIS A 139 
   PHE   0.013   0.003   PHE A  45 
   TYR   0.076   0.012   TYR A  89 
   ARG   0.029   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.001   HIS A 139 
   PHE   0.010   0.003   PHE A  67 
   TYR   0.062   0.014   TYR A  89 
   ARG   0.002   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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


  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 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: "   0"
    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 =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0081
  RMS(angles)           =   1.57
  MolProbity score      =   1.75

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: 59
        1.23 -     1.43: 413
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.44e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.44e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.27e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.18e+00
  bond model="   0" pdb=" ND1 HIS A 134 "
       model="   0" pdb=" CE1 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.15e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.31 -   106.11: 88
      106.11 -   111.91: 2530
      111.91 -   117.70: 462
      117.70 -   123.50: 849
      123.50 -   129.29: 150
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.58    4.02 1.00e+00 1.00e+00 1.61e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.48    4.72 1.30e+00 5.92e-01 1.32e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.11    3.49 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.90   -4.50 1.40e+00 5.10e-01 1.03e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.67   -3.07 1.00e+00 1.00e+00 9.41e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 974
       17.41 -    34.82: 41
       34.82 -    52.23: 13
       52.23 -    69.64: 4
       69.64 -    87.05: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  161.36   18.64     0      5.00e+00 4.00e-02 1.39e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.02   16.98     0      5.00e+00 4.00e-02 1.15e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.15   15.85     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 87
       0.050 -    0.100: 53
       0.100 -    0.150: 29
       0.150 -    0.200: 6
       0.200 -    0.250: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.05e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.25e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.065 2.00e-02 2.50e+03   2.57e-02 1.99e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.041 2.00e-02 2.50e+03   1.58e-02 7.50e+00
        model="   0" pdb=" CG  TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.10e+00
        model="   0" pdb=" CG  ASP A  36 "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 348
        2.30 -     2.87: 5096
        2.87 -     3.45: 5303
        3.45 -     4.02: 7116
        4.02 -     4.60: 10536
  Nonbonded interactions: 28399
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A  49 "
            model="   0" pdb=" HZ3 LYS A 125 "
     model   vdw
     1.719 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.768 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.769 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.773 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.806 1.850
  ... (remaining 28394 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 ==============================

        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 =   1.46 %
                favored =  94.16 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.57
  MolProbity score      =   1.65

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=  0.000)
  Max. delta:    0.039 (Z=  2.497)
  Mean delta:    0.011 (Z=  0.595)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.130 (Z=  3.975)
  Mean delta:    1.591 (Z=  0.865)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.054
  Max. delta:   85.748
  Mean delta:   12.146

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.251
  Mean delta:    0.075

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.423
    Angle     :  1.537   7.130   4079  Z= 0.663
    Chirality :  0.075   0.251    176
    Planarity :  0.008   0.043    327
    Dihedral  : 11.419  85.748    769
    Min Nonbonded Distance : 1.707
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  8.03 %
      Favored  : 90.51 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.00 %
      Favored  : 99.19 %
    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: -0.20 (0.70), residues: 137
    helix: -0.12 (0.53), residues: 75
    sheet:  None (None), residues: 0
    loop :  0.07 (0.89), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.008   0.003   PHE A  67 
   TYR   0.070   0.010   TYR A 111 
   ARG   0.040   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.007   0.002   PHE A  67 
   TYR   0.058   0.012   TYR A 111 
   ARG   0.005   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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

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

  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (68.606, 72.083, 51.064, 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: "   0"
    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 =   1.46 %
                favored =  90.51 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.54
  MolProbity score      =   1.73

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}

  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: 1.11 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}
  Time building chain proxies: 0.83, per 1000 atoms: 0.37
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (58.722, 59.136, 50.927, 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     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
    None
  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: 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 -     1.04: 1106
        1.04 -     1.23: 102
        1.23 -     1.43: 370
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.11e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.81e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.73e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.20e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.16e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.09 -   104.90: 35
      104.90 -   111.70: 2542
      111.70 -   118.50: 577
      118.50 -   125.31: 884
      125.31 -   132.11: 41
  Bond angle restraints: 4079
  Sorted by residual:
  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  132.11  -10.41 1.80e+00 3.09e-01 3.34e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.68    3.92 1.00e+00 1.00e+00 1.54e+01
  angle model="   0" pdb=" N   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
        model="   0" pdb=" C   LEU A 119 "
      ideal   model   delta    sigma   weight residual
     111.00  121.66  -10.66 2.80e+00 1.28e-01 1.45e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.80    3.80 1.00e+00 1.00e+00 1.45e+01
  angle model="   0" pdb=" C   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
        model="   0" pdb=" HA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     109.00   98.09   10.91 3.00e+00 1.11e-01 1.32e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.83: 951
       16.83 -    33.67: 59
       33.67 -    50.50: 15
       50.50 -    67.34: 7
       67.34 -    84.17: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  PRO A 117 "
           model="   0" pdb=" C   PRO A 117 "
           model="   0" pdb=" N   ASP A 118 "
           model="   0" pdb=" CA  ASP A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.26  -28.74     0      5.00e+00 4.00e-02 3.30e+01
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.19  -24.81     0      5.00e+00 4.00e-02 2.46e+01
  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  159.63   20.37     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 125
       0.089 -    0.177: 48
       0.177 -    0.265: 2
       0.265 -    0.353: 0
       0.353 -    0.441: 1
  Chirality restraints: 176
  Sorted by residual:
  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    2.07    0.44 2.00e-01 2.50e+01 4.87e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    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="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.00e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.191 2.00e-02 2.50e+03   8.11e-02 1.97e+02
        model="   0" pdb=" CG  TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.155 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.077 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.034 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.062 2.00e-02 2.50e+03   2.94e-02 2.60e+01
        model="   0" pdb=" CG  TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.024 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.046 2.00e-02 2.50e+03   1.75e-02 9.17e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 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 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 362
        2.31 -     2.88: 512  Time building chain proxies: 1.27, per 1000 atoms: 0.57
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.132, 53.428, 68.564, 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.
3
        2.88 -     3.45: 5273
        3.45 -     4.03: 6861
        4.03 -     4.60: 10233
  Nonbonded interactions: 27852
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.765 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.789 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.816 1.850
  nonbonded model="   0" pdb=" HB3 LEU A   3 "
            model="   0" pdb="HD22 LEU A  53 "
     model   vdw
     1.824 2.440
  ... (remaining 27847 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: 1.01
  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.


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

  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="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.36e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.76e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.74e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.63e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.22 -   106.00: 83
      106.00 -   111.77: 2493
      111.77 -   117.54: 493
      117.54 -   123.32: 824
      123.32 -   129.09: 186
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.41    4.19 1.00e+00 1.00e+00 1.75e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.46    4.74 1.30e+00 5.92e-01 1.33e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.15   -3.55 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.22    3.38 1.00e+00 1.00e+00 1.14e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.09   -4.69 1.40e+00 5.10e-01 1.12e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 976
       17.30 -    34.59: 38
       34.59 -    51.89: 14
       51.89 -    69.18: 4
       69.18 -    86.48: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.75   20.25     0      5.00e+00 4.00e-02 1.64e+01
  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  160.99   19.01     0      5.00e+00 4.00e-02 1.45e+01
  dihedral model="   0" pdb=" CA  PRO A 117 "
           model="   0" pdb=" C   PRO A 117 "
           model="   0" pdb=" N   ASP A 118 "
           model="   0" pdb=" CA  ASP A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.52   17.48     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.039: 80
       0.039 -    0.077: 39
       0.077 -    0.116: 32
       0.116 -    0.154: 20
       Time building chain proxies: 1.07, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.797, 48.931, 41.659, 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.
  0.154 -    0.192: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.25e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.12e-01
  chirality model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" C   THR A  82 "
            model="   0" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.69   -0.16 2.00e-01 2.50e+01 6.70e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.080 2.00e-02 2.50e+03   3.48e-02 3.64e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.022 2.00e-02 2.50e+03   4.40e-02 1.94e+01
        model="   0" pdb=" CG  ASP A  36 "    0.076 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.061 2.00e-02 2.50e+03   2.41e-02 1.75e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 121
        2.18 -     2.78: 4232
        2.78 -     3.39: 6046
        3.39 -     3.99: 7245
        3.99 -     4.60: 10997
  Nonbonded interactions: 28641
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.573 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.651 1.850
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.670 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.691 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.722 1.850
  ... (remaining 28636 not shown)

  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: (77.4, 40.091, 55.259, 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 ==============================

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 99
        1.23 -     1.43: 373
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.75e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.74e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.24e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.91e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.59e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.33 -   106.08: 87
      106.08 -   111.82: 2503
      111.82 -   117.57: 476
      117.57 -   123.32: 836
      123.32 -   129.07: 177
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.65    3.95 1.00e+00 1.00e+00 1.56e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.77    3.83 1.00e+00 1.00e+00 1.47e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.31    4.89 1.30e+00 5.92e-01 1.41e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.10   -3.50 1.00e+00 1.00e+00 1.23e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.76    4.44 1.30e+00 5.92e-01 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.81: 977
       15.81 -    31.62: 38
       31.62 -    47.42: 13
       47.42 -    63.23: 3
       63.23 -    79.04: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  161.73   18.27     0      5.00e+00 4.00e-02 1.34e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.34   16.66     0      5.00e+00 4.00e-02 1.11e+01
  dihedral model="   0" pdb=" N   HIS A 136 "
           model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" CB  HIS A 136 "
           model="   0" pdb=" CG  HIS A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.21  -42.79     3      1.50e+01 4.44e-03 7.68e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.038: 80
       0.038 -    0.076: 37
       0.076 -    0.113: 33
       0.113 -    0.151: 18
       0.151 -    0.189: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.89e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.53e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.03e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.024 2.00e-02 2.50e+03   4.95e-02 2.45e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.086 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.030 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.062 2.00e-02 2.50e+03   2.46e-02 1.81e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.052 2.00e-02 2.50e+03   2.29e-02 1.57e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 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 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 127
        2.17 -     2.78: 4150
        2.78 -     3.39: 6067
        3.39 -     3.99: 7472
        3.99 -     4.60: 11268
  Nonbonded interactions: 29084
  Sorted by model distance:
  nonbonded model="   0" pdb=" HH  TYR A  81 "
            model="   0" pdb=" HH  TYR A  89 "
     model   vdw
     1.563 2.100
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.664 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.715 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.734 1.850
  nonbonded model="   0" pdb=" HH  TYR A  81 "
            model="   0" pdb=" OH  TYR A  89 "
     model   vdw
     1.774 1.850
  ... (remaining 29079 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}

  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: 0.71
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.84 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: 0.99 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: 109
        1.23 -     1.43: 363
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.47e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.46e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.08e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.05e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.93e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.20 -   105.94: 80
      105.94 -   111.68: 2476
      111.68 -   117.41: 511
      117.41 -   123.15: 794
      123.15 -   128.89: 218
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.39    4.21 1.00e+00 1.00e+00 1.77e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.81    3.79 1.00e+00 1.00e+00 1.43e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.52    4.68 1.30e+00 5.92e-01 1.30e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.73    4.47 1.30e+00 5.92e-01 1.18e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.98   -3.38 1.00e+00 1.00e+00 1.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 969
       17.63 -    35.25: 43
       35.25 -    52.88: 13
       52.88 -    70.51: 7
       70.51 -    88.14: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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  161.89   18.11     0      5.00e+00 4.00e-02 1.31e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.57   17.43     0      5.00e+00 4.00e-02 1.22e+01
  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  163.92   16.08     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.042: 79
       0.042 -    0.082: 45
       0.082 -    0.121: 37
       0.121 -    0.161: 12
       0.161 -    0.201: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.20e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.056 2.00e-02 2.50e+03   2.54e-02 1.93e+01
        model="   0" pdb=" CG  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.048 2.00e-02 2.50e+03   1.88e-02 1.06e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 203
        2.22 -     2.82: 4595
        2.82 -     3.41: 5910
        3.41 -     4.01: 7268
        4.01 -     4.60: 11065
  Nonbonded interactions: 29041
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.631 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.661 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.677 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.696 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.744 1.850
  ... (remaining 29036 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: 63
        1.23 -     1.43: 409
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.10e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" 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="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.06e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 4.97e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.97e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       97.20 -   103.58: 13
      103.58 -   109.96: 2099
      109.96 -   116.34: 902
      116.34 -   122.72: 774
      122.72 -   129.10: 291
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.69    3.91 1.00e+00 1.00e+00 1.53e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.51    4.69 1.30e+00 5.92e-01 1.30e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.57    4.63 1.30e+00 5.92e-01 1.27e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  115.99   -3.39 1.00e+00 1.00e+00 1.15e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.10   -4.70 1.40e+00 5.10e-01 1.13e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 973
       17.50 -    35.00: 46
       35.00 -    52.49: 11
       52.49 -    69.99: 2
       69.99 -    87.49: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.03   22.97     0      5.00e+00 4.00e-02 2.11e+01
  dihedral model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" C   ASP A 116 "
           model="   0" pdb=" N   PRO A 117 "
           model="   0" pdb=" CA  PRO A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.46  -21.54     0      5.00e+00 4.00e-02 1.86e+01
  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  161.31   18.69     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 85
       0.055 -    0.109: 63
       0.109 -    0.164: 21
       0.164 -    0.218: 5
       0.218 -    0.273: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality model="   0" pdb=" CA  PRO A 117 "
            model="   0" pdb=" N   PRO A 117 "
            model="   0" pdb=" C   PRO A 117 "
            model="   0" pdb=" CB  PRO A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.85e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.071 2.00e-02 2.50e+03   2.86e-02 2.45e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.053 2.00e-02 2.50e+03   2.35e-02 1.66e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.053 2.00e-02 2.50e+03   2.07e-02 1.29e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 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 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.28 -     1.94: 19
        1.94 -     2.61: 2366
        2.61 -     3.27: 6642
        3.27 -     3.94: 7891
        3.94 -     4.60: 12077
  Nonbonded interactions: 28995
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB1 ALA A  35 "
            model="   0" pdb=" HE1 MET A 128 "
     model   vdw
     1.278 2.440
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.667 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.739 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.746 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  29 "
            model="   0" pdb="HD22 ASN A  72 "
     model   vdw
     1.779 1.850
  ... (remaining 28990 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: 2218
  At special positions: 0
  Unit cell: (46.62, 48.983, 46.457, 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.


  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.

        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)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 2
        1.23 -     1.42: 463
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.024 1.40e-02 5.10e+03 2.83e+00
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.212  0.019 2.00e-02 2.50e+03 9.15e-01
  bond model="   0" pdb=" C   TYR A  12 "
       model="   0" pdb=" N   SER A  13 "
    ideal  model  delta    sigma   weight residual
    1.329  1.316  0.013 1.40e-02 5.10e+03 8.19e-01
  bond model="   0" pdb=" C   THR A  20 "
       model="   0" pdb=" N   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.329  1.317  0.012 1.40e-02 5.10e+03 7.60e-01
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.330 -0.009 1.00e-02 1.00e+04 7.55e-01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.50 -   106.65: 85
      106.65 -   112.79: 2654
      112.79 -   118.93: 466
      118.93 -   125.08: 832
      125.08 -   131.22: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  102.55    6.45 3.00e+00 1.11e-01 4.62e+00
  angle model="   0" pdb=" N   VAL A  41 "
        model="   0" pdb=" CA  VAL A  41 "
        model="   0" pdb=" HA  VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.00  104.02    5.98 3.00e+00 1.11e-01 3.97e+00
  angle model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" CB  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     111.60  107.80    3.80 2.00e+00 2.50e-01 3.61e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  104.33    5.67 3.00e+00 1.11e-01 3.58e+00
  angle model="   0" pdb=" N   ASP A  44 "
        model="   0" pdb=" CA  ASP A  44 "
        model="   0" pdb=" C   ASP A  44 "
      ideal   model   delta    sigma   weight residual
     111.00  116.19   -5.19 2.80e+00 1.28e-01 3.44e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 981
       16.00 -    31.99: 31
       31.99 -    47.99: 12
       47.99 -    63.98: 2
       63.98 -    79.98: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A 123 "
           model="   0" pdb=" CG  GLU A 123 "
           model="   0" pdb=" CD  GLU A 123 "
           model="   0" pdb=" OE1 GLU A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   76.45  -76.45     1      3.00e+01 1.11e-03 8.17e+00
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -74.13   74.13     1      3.00e+01 1.11e-03 7.75e+00
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -74.02   74.02     1      3.00e+01 1.11e-03 7.73e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 86
       0.040 -    0.080: 57
       0.080 -    0.120: 21
       0.120 -    0.160: 10
       0.160 -    0.200: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.95e-01
  chirality model="   0" pdb=" CA  PRO A 117 "
            model="   0" pdb=" N   PRO A 117 "
            model="   0" pdb=" C   PRO A 117 "
            model="   0" pdb=" CB  PRO A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.12e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.032 2.00e-02 2.50e+03   1.18e-02 4.20e+00
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.021 2.00e-02 2.50e+03   8.11e-03 1.97e+00
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 105 "   -0.019 2.00e-02 2.50e+03   7.28e-03 1.59e+00
        model="   0" pdb=" CG  TYR A 105 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 105 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 105 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 105 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 105 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 105 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 105 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 105 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 24
        2.00 -     2.65: 2925
        2.65 -     3.30: 6807
        3.30 -     3.95: 8146
        3.95 -     4.60: 12423
  Nonbonded interactions: 30325
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 LEU A 119 "
            model="   0" pdb=" OE1 GLU A 123 "
     model   vdw
     1.353 2.620
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.719 1.850
  nonbonded model="   0" pdb="HG12 ILE A  77 "
            model="   0" pdb="HG21 THR A  83 "
     model   vdw
     1.745 2.440
  nonbonded model="   0" pdb=" HE  ARG A  21 "
            model="   0" pdb=" OD2 ASP A  29 "
     model   vdw
     1.810 1.850
  nonbonded model="   0" pdb=" H   GLY A  94 "
            model="   0" pdb="HD13 LEU A  99 "
     model   vdw
     1.812 2.270
  ... (remaining 30320 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 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
    None
  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: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 110
        1.23 -     1.43: 362
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 7.00e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.97e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.90e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.75e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.55e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.62 -   106.30: 110
      106.30 -   111.99: 2514
      111.99 -   117.67: 460
      117.67 -   123.36: 834
      123.36 -   129.04: 161
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.45    4.15 1.00e+00 1.00e+00 1.72e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.39    4.81 1.30e+00 5.92e-01 1.37e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.04   -4.64 1.40e+00 5.10e-01 1.10e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.38    3.22 1.00e+00 1.00e+00 1.04e+01
  angle model="   0" pdb=" CA  ASP A  44 "
        model="   0" pdb=" CB  ASP A  44 "
        model="   0" pdb=" CG  ASP A  44 "
      ideal   model   delta    sigma   weight residual
     112.60  115.81   -3.21 1.00e+00 1.00e+00 1.03e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 974
       17.50 -    35.00: 46
       35.00 -    52.49: 10
       52.49 -    69.99: 2
       69.99 -    87.49: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.24   19.76     0      5.00e+00 4.00e-02 1.56e+01
  dihedral model="   0" pdb=" CA  HIS A 135 "
           model="   0" pdb=" C   HIS A 135 "
           model="   0" pdb=" N   HIS A 136 "
           model="   0" pdb=" CA  HIS A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.43   17.57     0      5.00e+00 4.00e-02 1.23e+01
  dihedral model="   0" pdb=" CA  HIS A  43 "
           model="   0" pdb=" C   HIS A  43 "
           model="   0" pdb=" N   ASP A  44 "
           model="   0" pdb=" CA  ASP A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.05   14.95     0      5.00e+00 4.00e-02 8.94e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.036: 74
       0.036 -    0.071: 32
       0.071 -    0.106: 40
       0.106 -    0.141: 24
       0.141 -    0.176: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.71e-01
  chirality model="   0" pdb=" CA  GLU A 133 "
            model="   0" pdb=" N   GLU A 133 "
            model="   0" pdb=" C   GLU A 133 "
            model="   0" pdb=" CB  GLU A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.74e-01
  chirality model="   0" pdb=" CA  SER A  90 "
            model="   0" pdb=" N   SER A  90 "
            model="   0" pdb=" C   SER A  90 "
            model="   0" pdb=" CB  SER A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.92e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.069 2.00e-02 2.50e+03   2.76e-02 2.28e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.053 2.00e-02 2.50e+03   2.31e-02 1.60e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.011 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 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.043 2.00e-02 2.50e+03   1.64e-02 8.04e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 143
        2.19 -     2.79: 4320
        2.79 -     3.39: 6078
        3.39 -     4.00: 7301
        4.00 -     4.60: 11195
  Nonbonded interactions: 29037
  Sorted by model distance:
  nonbonded model="   0" pdb=" HD3 PRO A  52 "
            model="   0" pdb=" HE1 HIS A 138 "
     model   vdw
     1.585 2.270
  nonbonded model="   0" pdb=" O   LYS A  79 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.624 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.682 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.740 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.779 1.850
  ... (remaining 29032 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 GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A TYR   91": "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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1113
        1.03 -     1.22: 0
        1.22 -     1.42: 462
        1.42 -     1.61: 669
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" CD  ARG A 127 "
       model="   0" 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="   0" pdb=" CZ  ARG A  58 "
       model="   0" 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="   0" pdb=" CZ  ARG A  58 "
       model="   0" 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="   0" pdb=" NE  ARG A  58 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       11.44 -    35.32: 1
       35.32 -    59.21: 0
       59.21 -    83.10: 0
       83.10 -   106.98: 37
      106.98 -   130.87: 4053
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   11.44   98.03 3.00e+00 1.11e-01 1.07e+03
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.30   -9.83 3.00e+00 1.11e-01 1.07e+01
  angle model="   0" pdb=" CA  GLY A  42 "
        model="   0" pdb=" N   GLY A  42 "
        model="   0" pdb=" H   GLY A  42 "
      ideal   model   delta    sigma   weight residual
     114.00  119.91   -5.91 3.00e+00 1.11e-01 3.88e+00
  angle model="   0" pdb=" CA  GLY A  87 "
        model="   0" pdb=" N   GLY A  87 "
        model="   0" pdb=" H   GLY A  87 "
      ideal   model   delta    sigma   weight residual
     114.00  119.91   -5.91 3.00e+00 1.11e-01 3.88e+00
  angle model="   0" pdb=" CA  GLY A 121 "
        model="   0" pdb=" N   GLY A 121 "
        model="   0" pdb=" H   GLY A 121 "
      ideal   model   delta    sigma   weight residual
     114.00  119.88   -5.88 3.00e+00 1.11e-01 3.84e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 817
       17.88 -    35.77: 106
       35.77 -    53.65: 83
       53.65 -    71.53: 26
       71.53 -    89.41: 7
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" 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="   0" pdb=" N   LEU A   3 "
           model="   0" pdb=" CA  LEU A   3 "
           model="   0" pdb=" CB  LEU A   3 "
           model="   0" 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="   0" pdb=" CA  MET A 128 "
           model="   0" pdb=" CB  MET A 128 "
           model="   0" pdb=" CG  MET A 128 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A 108 "
            model="   0" pdb=" N   ILE A 108 "
            model="   0" pdb=" C   ILE A 108 "
            model="   0" 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="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" 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="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" 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="   0" pdb=" CB  TYR A  50 "   -0.000 2.00e-02 2.50e+03   5.65e-04 9.59e-03
        model="   0" pdb=" CG  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.000 2.00e-02 2.50e+03   5.40e-04 8.74e-03
        model="   0" pdb=" CG  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.000 2.00e-02 2.50e+03   5.36e-04 8.62e-03
        model="   0" pdb=" CG  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.44: 1300
        2.44 -     2.98: 5214
        2.98 -     3.52: 5616
        3.52 -     4.06: 7070
        4.06 -     4.60: 9938
  Nonbonded interactions: 29138
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LYS A  27 "
            model="   0" pdb=" H   LEU A  31 "
     model   vdw
     1.904 1.850
  nonbonded model="   0" pdb=" O   LEU A   9 "
            model="   0" pdb=" H   SER A  13 "
     model   vdw
     1.918 1.850
  nonbonded model="   0" pdb=" O   LEU A 132 "
            model="   0" pdb=" H   HIS A 134 "
     model   vdw
     1.924 1.850
  nonbonded model="   0" pdb=" O   ILE A 108 "
            model="   0" pdb=" H   TYR A 111 "
     model   vdw
     1.936 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.962 1.850
  ... (remaining 29133 not shown)

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

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

  Time building chain proxies: 0.99, per 1000 atoms: 0.45
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (64.177, 54.927, 51.593, 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 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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      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: (47.786, 48.525, 58.679, 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
    None
  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 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: "   0"
    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, 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}

============================== 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...
  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 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.


  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.

        Number of residues, atoms: 139, 2224
          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)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 67
        1.23 -     1.43: 405
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.85e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.38e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.30e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.87e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.64e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.16 -   106.03: 88
      106.03 -   111.90: 2531
      111.90 -   117.77: 462
      117.77 -   123.63: 871
      123.63 -   129.50: 127
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   GLU A  84 "
        model="   0" pdb=" N   LYS A  85 "
        model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta    sigma   weight residual
     121.70  129.50   -7.80 1.80e+00 3.09e-01 1.88e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.43    4.77 1.30e+00 5.92e-01 1.35e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.10    3.50 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" C   HIS A 135 "
        model="   0" pdb=" N   HIS A 136 "
        model="   0" pdb=" CA  HIS A 136 "
      ideal   model   delta    sigma   weight residual
     121.70  127.90   -6.20 1.80e+00 3.09e-01 1.19e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.22    3.38 1.00e+00 1.00e+00 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 975
       17.44 -    34.87: 41
       34.87 -    52.31: 13
       52.31 -    69.75: 3
       69.75 -    87.18: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.88   34.12     0      5.00e+00 4.00e-02 4.66e+01
  dihedral model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" C   HIS A 137 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.69   29.31     0      5.00e+00 4.00e-02 3.44e+01
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.39   19.61     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 74
       0.042 -    0.083: 47
       0.083 -    0.124: 35
       0.124 -    0.166: 17
       Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 79
        1.23 -     1.43: 393
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.81e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.82e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.64e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 5.01e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.17 -   106.02: 107
      106.02 -   111.87: 2474
      111.87 -   117.72: 513
      117.72 -   123.57: 841
      123.57 -   129.43: 144
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  129.43   -7.73 1.80e+00 3.09e-01 1.84e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.01    3.59 1.00e+00 1.00e+00 1.29e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.12    3.48 1.00e+00 1.00e+00 1.21e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.04   -3.44 1.00e+00 1.00e+00 1.18e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.76    4.44 1.30e+00 5.92e-01 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 960
       16.74 -    33.49: 55
       33.49 -    50.23: 15
       50.23 -    66.97: 1
       66.97 -    83.71: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.26   28.74     0      5.00e+00 4.00e-02 3.30e+01
  dihedral model="   0" pdb=" CA  ILE A 122 "
           model="   0" pdb=" C   ILE A 122 "
           model="   0" pdb=" N   GLU A 123 "
           model="   0" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.30   25.70     0      5.00e+00 4.00e-02 2.64e+01
  dihedral model="   0" pdb=" CA  GLU A 123 "
           model="   0" pdb=" C   GLU A 123 "
           model="   0" pdb=" N   ALA A 124 "
           model="   0" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.82   25.18     0      5.00e+00 4.00e-02 2.54e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.037: 68
       0.037 -    0.073: 37
       0.073 -    0.109: 33
       0.109 -    0.145: 30
      0.166 -    0.207: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PRO A 114 "
            model="   0" pdb=" N   PRO A 114 "
            model="   0" pdb=" C   PRO A 114 "
            model="   0" pdb=" CB  PRO A 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality model="   0" pdb=" CA  GLU A 120 "
            model="   0" pdb=" N   GLU A 120 "
            model="   0" pdb=" C   GLU A 120 "
            model="   0" pdb=" CB  GLU A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.06e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.072 2.00e-02 2.50e+03   2.87e-02 2.47e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.021 2.00e-02 2.50e+03   4.39e-02 1.93e+01
        model="   0" pdb=" CG  ASP A  36 "    0.076 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.050 2.00e-02 2.50e+03   1.92e-02 1.11e+01
        model="   0" pdb=" CG  TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 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 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.11: 73
        2.11 -     2.73: 3753
        2.73 -     3.35: 6252
        3.35 -     3.98: 7582
        3.98 -     4.60: 11303
  Nonbonded interactions: 28963
  Sorted by model distance:
  nonbonded model="   0" pdb="HD13 LEU A 119 "
            model="   0" pdb=" HE3 LYS A 125 "
     model   vdw
     1.484 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.569 1.850
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.700 2.440
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.723 1.850
  ... (remaining 28958 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
   0.145 -    0.180: 8
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.13e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.09e-01
  chirality model="   0" pdb=" CA  GLU A 123 "
            model="   0" pdb=" N   GLU A 123 "
            model="   0" pdb=" C   GLU A 123 "
            model="   0" pdb=" CB  GLU A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.22e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.075 2.00e-02 2.50e+03   3.05e-02 2.79e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.021 2.00e-02 2.50e+03   4.27e-02 1.82e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.074 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.025 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.046 2.00e-02 2.50e+03   2.03e-02 1.24e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.007 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 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.31: 397
        2.31 -     2.88: 5191
        2.88 -     3.46: 5292
        3.46 -     4.03: 7052
        4.03 -     4.60: 10306
  Nonbonded interactions: 28238
  Sorted by model distance:
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.741 2.440
  nonbonded model="   0" pdb=" HZ2 LYS A 109 "
            model="   0" pdb=" OD1 ASP A 110 "
     model   vdw
     1.745 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.758 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.760 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.780 1.850
  ... (remaining 28233 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: 2218
  At special positions: 0
  Unit cell: (46.682, 45.827, 59.996, 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.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 7
        1.23 -     1.42: 458
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   LYS A  79 "
       model="   0" pdb=" N   GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.42e+00
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.09e+00
  bond model="   0" pdb=" C   HIS A 134 "
       model="   0" pdb=" N   HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.92e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.334 -0.013 1.00e-02 1.00e+04 1.57e+00
  bond model="   0" pdb=" C   THR A  82 "
       model="   0" pdb=" N   THR A  83 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.41e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.99 -   106.25: 46
      106.25 -   112.51: 2718
      112.51 -   118.77: 442
      118.77 -   125.02: 831
      125.02 -   131.28: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  123.19   -5.19 3.00e+00 1.11e-01 3.00e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.07   -5.07 3.00e+00 1.11e-01 2.86e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.65   -4.65 3.00e+00 1.11e-01 2.40e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.62   -4.62 3.00e+00 1.11e-01 2.37e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.46   -4.46 3.00e+00 1.11e-01 2.21e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.54: 987
       14.54 -    29.08: 22
       29.08 -    43.62: 12
       43.62 -    58.16: 8
       58.16 -    72.69: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A 133 "
           model="   0" pdb=" CG  GLU A 133 "
           model="   0" pdb=" CD  GLU A 133 "
           model="   0" pdb=" OE1 GLU A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   72.60  -72.60     1      3.00e+01 1.11e-03 7.48e+00
  dihedral model="   0" pdb=" CB  GLU A  75 "
           model="   0" pdb=" CG  GLU A  75 "
           model="   0" pdb=" CD  GLU A  75 "
           model="   0" pdb=" OE1 GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -68.21   68.21     1      3.00e+01 1.11e-03 6.71e+00
  dihedral model="   0" pdb=" CE1 TYR A  91 "
           model="   0" pdb=" CZ  TYR A  91 "
           model="   0" pdb=" OH  TYR A  91 "
           model="   0" pdb=" HH  TYR A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  107.31   72.69     2      3.00e+01 1.11e-03 4.86e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 128
       0.028 -    0.057: 30
       0.057 -    0.085: 7
       0.085 -    0.114: 8
       0.114 -    0.142: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.05e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.63e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.30e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.012 5.00e-02 4.00e+02   1.89e-02 5.74e-01
        model="   0" pdb=" N   PRO A   6 "    0.033 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.010 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.010 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.009 2.00e-02 2.50e+03   4.23e-03 5.36e-01
        model="   0" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.006 2.00e-02 2.50e+03   3.76e-03 4.24e-01
        model="   0" pdb=" CG  TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 101
        2.14 -     2.75: 4300
        2.75 -     3.37: 5819
        3.37 -     3.98: 7477
        3.98 -     4.60: 11367
  Nonbonded interactions: 29064
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  71 "
            model="   0" pdb="HD23 LEU A  99 "
     model   vdw
     1.520 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  47 "
            model="   0" pdb="HH21 ARG A 129 "
     model   vdw
     1.668 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.717 2.270
  nonbonded model="   0" pdb=" O   ASP A  88 "
            model="   0" pdb=" HH  TYR A  91 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.740 1.850
  ... (remaining 29059 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...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 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 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: "   0"
    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: (46.775, 49.696, 55.19, 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 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: "   0"
    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: 2224
  At special positions: 0
  Unit cell: (54.344, 53.947, 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    1113      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: 1.18 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: 50
        1.23 -     1.42: 422
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.71e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.45e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.95e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.29e+00
  bond model="   0" pdb=" ND1 HIS A 134 "
       model="   0" pdb=" CE1 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.98e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.41 -   106.16: 94
      106.16 -   111.91: 2533
      111.91 -   117.67: 448
      117.67 -   123.42: 844
      123.42 -   129.17: 160
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.74    3.86 1.00e+00 1.00e+00 1.49e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.29   -3.69 1.00e+00 1.00e+00 1.36e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.42    4.78 1.30e+00 5.92e-01 1.35e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.99    3.61 1.00e+00 1.00e+00 1.30e+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  128.06   -6.36 1.80e+00 3.09e-01 1.25e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 973
       17.03 -    34.06: 44
       34.06 -    51.10: 12
       51.10 -    68.13: 3
       68.13 -    85.16: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.94   23.06     0      5.00e+00 4.00e-02 2.13e+01
  dihedral model="   0" pdb=" CA  PRO A 117 "
           model="   0" pdb=" C   PRO A 117 "
           model="   0" pdb=" N   ASP A 118 "
           model="   0" pdb=" CA  ASP A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.29   20.71     0      5.00e+00 4.00e-02 1.72e+01
  dihedral model="   0" pdb=" CA  LYS A  85 "
           model="   0" pdb=" C   LYS A  85 "
           model="   0" pdb=" N   ILE A  86 "
           model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.96   15.04     0      5.00e+00 4.00e-02 9.05e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.035: 76
       0.035 -    0.069: 37
       0.069 -    0.104: 33
       0.104 -    0.138: 21
       0.138 -    0.172: 9
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.43e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.50e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.63e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.052 2.00e-02 2.50e+03   2.07e-02 1.29e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.043 2.00e-02 2.50e+03   1.62e-02 7.90e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  ASP A 116 "    0.014 2.00e-02 2.50e+03   2.79e-02 7.79e+00
        model="   0" pdb=" C   ASP A 116 "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" O   ASP A 116 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" N   PRO A 117 "    0.016 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 233
        2.24 -     2.83: 4677
        2.83 -     3.42: 5706
        3.42 -     4.01: 7001
        4.01 -     4.60: 10673
  Nonbonded interactions: 28290
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ILE A  71 "
            model="   0" pdb=" HE2 LYS A  79 "
     model   vdw
     1.654 2.620
  nonbonded model="   0" pdb=" HE1 TYR A  68 "
            model="   0" pdb=" HD3 LYS A  85 "
     model   vdw
     1.679 2.270
  nonbonded model="   0" pdb=" OE1 GLU A  32 "
            model="   0" pdb=" HZ2 LYS A  85 "
     model   vdw
     1.687 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.753 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.772 1.850
  ... (remaining 28285 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 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   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: "   0"
    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 -     1.22: 0
        1.22 -     1.42: 459
        1.42 -     1.61: 673
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ARG A 127 "
       model="   0" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.370 -0.041 1.40e-02 5.10e+03 8.61e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.363  0.015 1.10e-02 8.26e+03 1.97e+00
  bond model="   0" pdb=" C   GLN A 100 "
       model="   0" pdb=" N   LYS A 101 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.62e+00
  bond model="   0" pdb=" C   HIS A 137 "
       model="   0" pdb=" N   HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.49e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.48e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.37 -   106.63: 75
      106.63 -   112.89: 2671
      112.89 -   119.15: 463
      119.15 -   125.41: 828
      125.41 -   131.67: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  104.50    5.50 3.00e+00 1.11e-01 3.36e+00
  angle model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" CB  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     111.60  107.97    3.63 2.00e+00 2.50e-01 3.30e+00
  angle model="   0" pdb=" N   LYS A 109 "
        model="   0" pdb=" CA  LYS A 109 "
        model="   0" pdb=" HA  LYS A 109 "
      ideal   model   delta    sigma   weight residual
     110.00  104.57    5.43 3.00e+00 1.11e-01 3.27e+00
  angle model="   0" pdb=" N   VAL A  41 "
        model="   0" pdb=" CA  VAL A  41 "
        model="   0" pdb=" HA  VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.00  104.58    5.42 3.00e+00 1.11e-01 3.27e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  123.07   -5.07 3.00e+00 1.11e-01 2.85e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 981
       17.48 -    34.96: 23
       34.96 -    52.45: 21
       52.45 -    69.93: 3
       69.93 -    87.41: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.41   87.41     1      3.00e+01 1.11e-03 1.02e+01
  dihedral model="   0" pdb=" CB  GLU A 120 "
           model="   0" pdb=" CG  GLU A 120 "
           model="   0" pdb=" CD  GLU A 120 "
           model="   0" pdb=" OE1 GLU A 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.93   86.93     1      3.00e+01 1.11e-03 1.01e+01
  dihedral model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" CB  HIS A 138 "
           model="   0" pdb=" CG  HIS A 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  104.66  -44.66     3      1.50e+01 4.44e-03 8.03e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 81
       0.040 -    0.080: 56
       0.080 -    0.119: 26
       0.119 -    0.159: 9
       0.159 -    0.199: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.88e-01
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.92e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.74e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.039 2.00e-02 2.50e+03   1.47e-02 6.46e+00
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.024 2.00e-02 2.50e+03   9.50e-03 2.71e+00
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.000 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 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 105 "   -0.024 2.00e-02 2.50e+03   9.14e-03 2.51e+00
        model="   0" pdb=" CG  TYR A 105 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 105 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 105 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 105 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 105 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 105 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 105 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 105 "    0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.34 -     1.99: 22
        1.99 -     2.65: 2825
        2.65 -     3.30: 6605
        3.30 -     3.95: 7839
        3.95 -     4.60: 12015
  Nonbonded interactions: 29306
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE1 PHE A  67 "
            model="   0" pdb="HD22 LEU A  99 "
     model   vdw
     1.343 2.270
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" HB2 ASP A  44 "
     model   vdw
     1.617 2.440
  nonbonded model="   0" pdb="HD11 ILE A  86 "
            model="   0" pdb=" HA  LYS A 125 "
     model   vdw
     1.665 2.440
  nonbonded model="   0" pdb=" O   VAL A  41 "
            model="   0" pdb=" H   LYS A 113 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb="HD11 LEU A  39 "
            model="   0" pdb="HD11 ILE A 122 "
     model   vdw
     1.737 2.440
  ... (remaining 29301 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: (73.109, 41.606, 48.597, 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.
Symmetry information was not found, putting molecule in P1 box.

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

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (77.701, 37.609, 53.607, 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: 0.97
  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.

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: 53
        1.23 -     1.42: 419
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.45e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.86e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.89e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.26e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.302  0.028 1.30e-02 5.92e+03 4.72e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.60 -   105.52: 52
      105.52 -   111.44: 2429
      111.44 -   117.36: 577
      117.36 -   123.28: 838
      123.28 -   129.20: 183
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.94    3.66 1.00e+00 1.00e+00 1.34e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.95   -3.35 1.00e+00 1.00e+00 1.12e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.95    4.25 1.30e+00 5.92e-01 1.07e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.95   -4.55 1.40e+00 5.10e-01 1.06e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.43    3.17 1.00e+00 1.00e+00 1.00e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 976
       16.97 -    33.94: 43
       33.94 -    50.91: 9
       50.91 -    67.88: 4
       67.88 -    84.85: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  163.83   16.17     0      5.00e+00 4.00e-02 1.05e+01
  dihedral model="   0" pdb=" CB  MET A 128 "
           model="   0" pdb=" CG  MET A 128 "
           model="   0" pdb=" SD  MET A 128 "
           model="   0" pdb=" CE  MET A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  125.01   54.99     3      1.50e+01 4.44e-03 9.32e+00
  dihedral model="   0" pdb=" CA  LYS A 113 "
           model="   0" pdb=" C   LYS A 113 "
           model="   0" pdb=" N   PRO A 114 "
           model="   0" pdb=" CA  PRO A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.94   15.06     0      5.00e+00 4.00e-02 9.08e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 78
       0.044 -    0.087: 48
       0.087 -    0.130: 36
       0.130 -    0.173: 13
       0.173 -    0.216: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality model="   0" pdb=" CA  ASP A  44 "
            model="   0" pdb=" N   ASP A  44 "
            model="   0" pdb=" C   ASP A  44 "
            model="   0" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.12e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.61e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.088 2.00e-02 2.50e+03   3.60e-02 3.89e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.008 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 "   -0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.045 2.00e-02 2.50e+03   2.25e-02 1.52e+01
        model="   0" pdb=" CG  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.022 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.043 2.00e-02 2.50e+03   1.65e-02 8.17e+00
        model="   0" pdb=" CG  TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.002 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 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.012 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.37 -     2.02: 29
        2.02 -     2.66: 3066
        2.66 -     3.31: 6451
        3.31 -     3.95: 7715
        3.95 -     4.60: 11827
  Nonbonded interactions: 29088
  Sorted by model distance:
  nonbonded model="   0" pdb="HD22 LEU A  39 "
            model="   0" pdb=" HA  ALA A 124 "
     model   vdw
     1.374 2.440
  nonbonded model="   0" pdb=" HE2 TYR A  91 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.382 2.270
  nonbonded model="   0" pdb="HD11 LEU A  39 "
            model="   0" pdb=" HG3 MET A 128 "
     model   vdw
     1.582 2.440
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.678 1.850
  nonbonded model="   0" pdb=" OE2 GLU A   8 "
            model="   0" pdb="HH21 ARG A  58 "
     model   vdw
     1.703 1.850
  ... (remaining 29083 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 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: "   0"
    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: 1.04
  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.

        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}
        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 -     1.43: 412
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.86e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.67e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.06e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.88e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.85e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.96 -   105.91: 82
      105.91 -   111.87: 2509
      111.87 -   117.82: 490
      117.82 -   123.77: 882
      123.77 -   129.73: 116
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  129.73   -8.03 1.80e+00 3.09e-01 1.99e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.14   -3.54 1.00e+00 1.00e+00 1.25e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.09   -4.69 1.40e+00 5.10e-01 1.12e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.26    3.34 1.00e+00 1.00e+00 1.12e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.28    3.32 1.00e+00 1.00e+00 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 975
       17.39 -    34.77: 45
       34.77 -    52.16: 10
       52.16 -    69.54: 2
       69.54 -    86.93: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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  154.67   25.33     0      5.00e+00 4.00e-02 2.57e+01
  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  156.16   23.84     0      5.00e+00 4.00e-02 2.27e+01
  dihedral model="   0" pdb=" CA  LYS A 113 "
           model="   0" pdb=" C   LYS A 113 "
           model="   0" pdb=" N   PRO A 114 "
           model="   0" pdb=" CA  PRO A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.65   17.35     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 78
       0.046 -    0.091: 45
       0.091 -    0.136: 41
       0.136 -    0.182: 9
       0.182 -    0.227: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.58e-01
  chirality model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.26e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.076 2.00e-02 2.50e+03   3.23e-02 3.13e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.061 2.00e-02 2.50e+03   2.39e-02 1.72e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.020 2.00e-02 2.50e+03   4.05e-02 1.64e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.070 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.024 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 93
        2.12 -     2.74: 3884
        2.74 -     3.36: 6150
        3.36 -     3.98: 7433
        3.98 -     4.60: 11215
  Nonbonded interactions: 28775
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.504 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.709 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.717 1.850
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.738 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.746 1.850
  ... (remaining 28770 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...
  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.


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=  2.810)
  Mean delta:    0.012 (Z=  0.626)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.999 (Z=  4.126)
  Mean delta:    1.647 (Z=  0.881)

                      ----------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   152.35    27.65  5.00e+00  3.06e+01   5.5*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00  -152.51   -27.49  5.00e+00  3.02e+01   5.5*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   153.62    26.38  5.00e+00  2.78e+01   5.3*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -156.11   -23.89  5.00e+00  2.28e+01   4.8*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   156.31    23.69  5.00e+00  2.24e+01   4.7*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   158.55    21.45  5.00e+00  1.84e+01   4.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   159.67    20.33  5.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.047
  Max. delta:   85.881
  Mean delta:   11.941

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.206
  Mean delta:    0.075

                       ----------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            0.070       0.130       98.12   6.5*sigma

  Min. delta:    0.000
  Max. delta:    0.070
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.446
    Angle     :  1.574   6.999   4079  Z= 0.674
    Chirality :  0.075   0.206    176
    Planarity :  0.008   0.065    327
    Dihedral  : 10.477  85.881    769
    Min Nonbonded Distance : 1.587
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  5.84 %
      Favored  : 90.51 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  1.61 %
      Favored  : 97.58 %
    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: -0.31 (0.71), residues: 137
    helix: -0.11 (0.51), residues: 80
    sheet:  None (None), residues: 0
    loop : -0.11 (0.96), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.013   0.003   PHE A  45 
   TYR   0.160   0.016   TYR A  89 
   ARG   0.037   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.009   0.003   PHE A  67 
   TYR   0.130   0.020   TYR A  89 
   ARG   0.003   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.164, 54.967, 44.33, 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: (45.874, 77.124, 40.293, 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: 2
        1.23 -     1.42: 463
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   LEU A   2 "
       model="   0" pdb=" N   LEU A   3 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.44e+00
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.466  0.025 2.10e-02 2.27e+03 1.44e+00
  bond model="   0" pdb=" C   LEU A  93 "
       model="   0" pdb=" N   GLY A  94 "
    ideal  model  delta    sigma   weight residual
    1.329  1.344 -0.015 1.40e-02 5.10e+03 1.19e+00
  bond model="   0" pdb=" C   LEU A  25 "
       model="   0" pdb=" N   LEU A  26 "
    ideal  model  delta    sigma   weight residual
    1.329  1.343 -0.014 1.40e-02 5.10e+03 1.01e+00
  bond model="   0" pdb=" C   ASP A  29 "
       model="   0" pdb=" N   ILE A  30 "
    ideal  model  delta    sigma   weight residual
    1.329  1.343 -0.014 1.40e-02 5.10e+03 1.00e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.34 -   106.47: 48
      106.47 -   112.60: 2714
      112.60 -   118.73: 437
      118.73 -   124.86: 838
      124.86 -   131.00: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.84    5.16 3.00e+00 1.11e-01 2.96e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.94    5.06 3.00e+00 1.11e-01 2.84e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.56   -4.56 3.00e+00 1.11e-01 2.31e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.50   -4.50 3.00e+00 1.11e-01 2.25e+00
  angle model="   0" pdb=" C   PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  104.64    4.36 3.00e+00 1.11e-01 2.12e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.34: 987
       14.34 -    28.69: 26
       28.69 -    43.03: 15
       43.03 -    57.37: 3
       57.37 -    71.72: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CE1 TYR A  81 "
           model="   0" pdb=" CZ  TYR A  81 "
           model="   0" pdb=" OH  TYR A  81 "
           model="   0" pdb=" HH  TYR A  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  108.28   71.72     2      3.00e+01 1.11e-03 4.81e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -111.75  -68.25     2      3.00e+01 1.11e-03 4.60e+00
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  171.51    8.49     0      5.00e+00 4.00e-02 2.88e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 106
       0.023 -    0.046: 45
       0.046 -    0.069: 10
       0.069 -    0.092: 12
       0.092 -    0.115: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.31e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.03e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.10 2.00e-01 2.50e+01 2.75e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.015 5.00e-02 4.00e+02   2.26e-02 8.18e-01
        model="   0" pdb=" N   PRO A   6 "   -0.039 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.013 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.001 2.00e-02 2.50e+03   4.62e-03 6.42e-01
        model="   0" pdb=" CG  TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "   -0.013 5.00e-02 4.00e+02   1.93e-02 5.94e-01
        model="   0" pdb=" N   PRO A  54 "    0.033 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "   -0.010 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.37 -     2.02: 31
        2.02 -     2.66: 3117
        2.66 -     3.31: 6617
        3.31 -     3.95: 7900
        3.95 -     4.60: 12522
  Nonbonded interactions: 30187
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" HB3 GLU A  49 "
     model   vdw
     1.372 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.644 1.850
  nonbonded model="   0" pdb=" HH  TYR A 105 "
            model="   0" pdb=" OE2 GLU A 120 "
     model   vdw
     1.681 1.850
  nonbonded model="   0" pdb=" O   GLY A  42 "
            model="   0" pdb=" HZ1 LYS A 125 "
     model   vdw
     1.730 1.850
  nonbonded model="   0" pdb=" HE2 TYR A 105 "
            model="   0" pdb=" HE3 LYS A 109 "
     model   vdw
     1.739 2.270
  ... (remaining 30182 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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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: (49.278, 44.956, 52.428, 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 =  90.51 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.57
  MolProbity score      =   1.73

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 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: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      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 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: "   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: 0.86
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.98 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: 1113
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" CZ  ARG A  58 "
       model="   0" 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="   0" pdb=" CZ  ARG A  58 "
       model="   0" 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="   0" pdb=" CZ  ARG A 129 "
       model="   0" 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="   0" pdb=" NE  ARG A 127 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       57.74 -    72.44: 1
       72.44 -    87.14: 0
       87.14 -   101.84: 2
      101.84 -   116.53: 3008
      116.53 -   131.23: 1080
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   57.74   51.73 3.00e+00 1.11e-01 2.97e+02
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  131.23  -21.76 3.00e+00 1.11e-01 5.26e+01
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.16   -9.69 3.00e+00 1.11e-01 1.04e+01
  angle model="   0" pdb=" CA  GLY A 121 "
        model="   0" pdb=" N   GLY A 121 "
        model="   0" pdb=" H   GLY A 121 "
      ideal   model   delta    sigma   weight residual
     114.00  119.89   -5.89 3.00e+00 1.11e-01 3.85e+00
  angle model="   0" pdb=" CA  GLY A  73 "
        model="   0" pdb=" N   GLY A  73 "
        model="   0" pdb=" H   GLY A  73 "
      ideal   model   delta    sigma   weight residual
     114.00  119.86   -5.86 3.00e+00 1.11e-01 3.81e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 817
       17.05 -    34.10: 101
       34.10 -    51.15: 70
       51.15 -    68.19: 42
       68.19 -    85.24: 9
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A 133 "
           model="   0" pdb=" CG  GLU A 133 "
           model="   0" pdb=" CD  GLU A 133 "
           model="   0" 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="   0" pdb=" CB  ARG A  58 "
           model="   0" pdb=" CG  ARG A  58 "
           model="   0" pdb=" CD  ARG A  58 "
           model="   0" 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="   0" pdb=" N   GLU A   8 "
           model="   0" pdb=" CA  GLU A   8 "
           model="   0" pdb=" CB  GLU A   8 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" 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="   0" pdb=" CA  ILE A  38 "
            model="   0" pdb=" N   ILE A  38 "
            model="   0" pdb=" C   ILE A  38 "
            model="   0" 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="   0" pdb=" CA  ILE A  71 "
            model="   0" pdb=" N   ILE A  71 "
            model="   0" pdb=" C   ILE A  71 "
            model="   0" 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="   0" pdb=" CB  TYR A  91 "   -0.000 2.00e-02 2.50e+03   5.47e-04 8.97e-03
        model="   0" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.000 2.00e-02 2.50e+03   5.46e-04 8.94e-03
        model="   0" pdb=" CG  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 105 "   -0.000 2.00e-02 2.50e+03   5.28e-04 8.38e-03
        model="   0" pdb=" CG  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 105 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 105 "    0.000 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.45: 1300
        2.45 -     2.98: 5127
        2.98 -     3.52: 5387
        3.52 -     4.06: 6745
        4.06 -     4.60: 9591
  Nonbonded interactions: 28150
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   PRO A 117 "
            model="   0" pdb=" H   LEU A 119 "
     model   vdw
     1.908 1.850
  nonbonded model="   0" pdb=" O   ILE A 108 "
            model="   0" pdb=" H   TYR A 111 "
     model   vdw
     1.908 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.913 1.850
  nonbonded model="   0" pdb=" O   LYS A 125 "
            model="   0" pdb=" H   ARG A 129 "
     model   vdw
     1.928 1.850
  nonbonded model="   0" pdb=" O   LEU A   9 "
            model="   0" pdb=" H   SER A  13 "
     model   vdw
     1.931 1.850
  ... (remaining 28145 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 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: 2224
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2224
      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: 0.89
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.02 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: 1.02
  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.

        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: 1.02, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.441, 48.166, 54.157, 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: "   0"
    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: 2
        1.23 -     1.42: 462
        1.42 -     1.61: 668
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.40e-02 5.10e+03 3.05e+00
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.390 -0.016 1.10e-02 8.26e+03 2.14e+00
  bond model="   0" pdb=" C   LEU A  93 "
       model="   0" pdb=" N   GLY A  94 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.40e-02 5.10e+03 2.04e+00
  bond model="   0" pdb=" C   ILE A  78 "
       model="   0" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.40e-02 5.10e+03 2.01e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.335 -0.014 1.00e-02 1.00e+04 1.92e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.40 -   106.52: 49
      106.52 -   112.63: 2704
      112.63 -   118.75: 441
      118.75 -   124.87: 842
      124.87 -   130.99: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   GLU A 133 "
        model="   0" pdb=" N   HIS A 134 "
        model="   0" pdb=" CA  HIS A 134 "
      ideal   model   delta    sigma   weight residual
     121.70  125.18   -3.48 1.80e+00 3.09e-01 3.73e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.24   -5.24 3.00e+00 1.11e-01 3.05e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" N   ASP A 118 "
        model="   0" pdb=" CA  ASP A 118 "
      ideal   model   delta    sigma   weight residual
     121.70  124.82   -3.12 1.80e+00 3.09e-01 3.01e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  114.11   -5.11 3.00e+00 1.11e-01 2.90e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.90    5.10 3.00e+00 1.11e-01 2.89e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.64: 989
       16.64 -    33.28: 29
       33.28 -    49.93: 9
       49.93 -    66.57: 2
       66.57 -    83.21: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A 120 "
           model="   0" pdb=" CG  GLU A 120 "
           model="   0" pdb=" CD  GLU A 120 "
           model="   0" pdb=" OE1 GLU A 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.21  -83.21     1      3.00e+01 1.11e-03 9.41e+00
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -80.19   80.19     1      3.00e+01 1.11e-03 8.85e+00
  dihedral model="   0" pdb=" CG  LYS A  63 "
           model="   0" pdb=" CD  LYS A  63 "
           model="   0" pdb=" CE  LYS A  63 "
           model="   0" pdb=" NZ  LYS A  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -105.89   45.89     3      1.50e+01 4.44e-03 8.25e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 114
       0.030 -    0.059: 44
       0.059 -    0.089: 9
       0.089 -    0.118: 6
       0.        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 131}
118 -    0.148: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.45e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.53e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.015 5.00e-02 4.00e+02   2.28e-02 8.28e-01
        model="   0" pdb=" N   PRO A   6 "   -0.039 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.013 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.002 2.00e-02 2.50e+03   4.92e-03 7.25e-01
        model="   0" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.003 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 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 135 "    0.009 2.00e-02 2.50e+03   6.01e-03 7.23e-01
        model="   0" pdb=" CG  HIS A 135 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 135 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 135 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 135 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 135 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 135 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 135 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.13: 82
        2.13 -     2.75: 4077
        2.75 -     3.37: 6105
        3.37 -     3.98: 7575
        3.98 -     4.60: 11698
  Nonbonded interactions: 29537
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.519 1.850
  nonbonded model="   0" pdb=" OE2 GLU A 123 "
            model="   0" pdb=" HE  ARG A 127 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb=" HE2 LYS A  85 "
            model="   0" pdb=" HA  ASP A  88 "
     model   vdw
     1.733 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.780 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.814 1.850
  ... (remaining 29532 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:    0.024 (Z=  1.728)
  Mean delta:    0.006 (Z=  0.344)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.281 (Z=  1.615)
  Mean delta:    0.854 (Z=  0.421)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   89.748
  Mean delta:   10.611

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.142
  Mean delta:    0.044

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.021
  Mean delta:    0.004

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.004   0.024   2242  Z= 0.245
    Angle     :  1.158   5.262   4079  Z= 0.431
    Chirality :  0.044   0.142    176
    Planarity :  0.003   0.021    327
    Dihedral  : 10.224  89.748    769
    Min Nonbonded Distance : 1.641
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.81 %
      Favored  : 99.19 %
    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:  1.63 (0.68), residues: 137
    helix:  0.73 (0.54), residues: 86
    sheet: -0.41 (1.48), residues: 10
    loop :  2.82 (0.88), residues: 41
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.007   0.002   PHE A  67 
   TYR   0.019   0.004   TYR A 111 
   ARG   0.011   0.002   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.005   0.002   PHE A  67 
   TYR   0.017   0.004   TYR A 111 
   ARG   0.001   0.000   ARG A  58 

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

   A 139  HIS

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 1
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.304  0.025 1.40e-02 5.10e+03 3.10e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.335 -0.014 1.00e-02 1.00e+04 1.84e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.51e+00
  bond model="   0" pdb=" C   ILE A  51 "
       model="   0" pdb=" N   PRO A  52 "
    ideal  model  delta    sigma   weight residual
    1.341  1.322  0.019 1.60e-02 3.91e+03 1.45e+00
  bond model="   0" pdb=" C   HIS A 137 "
       model="   0" pdb=" N   HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.40e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.15 -   106.34: 43
      106.34 -   112.53: 2730
      112.53 -   118.72: 432
      118.72 -   124.91: 832
      124.91 -   131.10: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.87   -4.87 3.00e+00 1.11e-01 2.63e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  104.23    4.77 3.00e+00 1.11e-01 2.53e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.46   -4.46 3.00e+00 1.11e-01 2.21e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  104.56    4.44 3.00e+00 1.11e-01 2.19e+00
  angle model="   0" pdb=" C   PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  104.75    4.25 3.00e+00 1.11e-01 2.01e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 994
       16.01 -    32.01: 23
       32.01 -    48.02: 11
       48.02 -    64.02: 2
       64.02 -    80.03: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -67.70   67.70     1      3.00e+01 1.11e-03 6.62e+00
  dihedral model="   0" pdb=" CE1 TYR A  50 "
           model="   0" pdb=" CZ  TYR A  50 "
           model="   0" pdb=" OH  TYR A  50 "
           model="   0" pdb=" HH  TYR A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   99.97   80.03     2      3.00e+01 1.11e-03 5.17e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -104.46  -75.54     2      3.00e+01 1.11e-03 5.00e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 126
       0.027 -    0.055: 30
       0.055 -    0.082: 9
       0.082 -    0.109: 8
       0.109 -    0.137: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.68e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.00e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.013 5.00e-02 4.00e+02   2.00e-02 6.39e-01
        model="   0" pdb=" N   PRO A   6 "    0.035 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.010 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.011 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "   -0.012 5.00e-02 4.00e+02   1.86e-02 5.54e-01
        model="   0" pdb=" N   PRO A  54 "    0.032 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "   -0.010 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "   -0.010 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 138 "   -0.002 2.00e-02 2.50e+03   4.46e-03 3.98e-01
        model="   0" pdb=" CG  HIS A 138 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 138 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 138 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 138 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 138 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 138 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 138 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 263
        2.27 -     2.85: 5147
        2.85 -     3.43: 5375
        3.43 -     4.02: 7362
        4.02 -     4.60: 11066
  Nonbonded interactions: 29213
  Sorted by model distance:
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD11 ILE A  77 "
     model   vdw
     1.687 2.440
  nonbonded model="   0" pdb=" HB3 ASP A  74 "
            model="   0" pdb="HG13 ILE A  77 "
     model   vdw
     1.766 2.440
  nonbonded model="   0" pdb=" H   TYR A  91 "
            model="   0" pdb=" O   LEU A  99 "
     model   vdw
     1.771 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.803 2.270
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.823 1.850
  ... (remaining 29208 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.82, per 1000 atoms: 0.37
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.98, 66.89, 45.642, 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   24": "OE1" <-> "OE2"
    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: "   0"
    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: 0.76, per 1000 atoms: 0.34
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.187, 50.463, 71.886, 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 =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0043
  RMS(angles)           =   1.16
  MolProbity score      =   1.35

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...
  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: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.11 seconds

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

        Number of residues, atoms: 139, 2224
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 1.06, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.614, 51.599, 60.533, 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: 5
        1.23 -     1.42: 460
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.75e+00
  bond model="   0" pdb=" C   ILE A 131 "
       model="   0" pdb=" N   LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.54e+00
  bond model="   0" pdb=" C   TYR A 111 "
       model="   0" pdb=" N   VAL A 112 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.47e+00
  bond model="   0" pdb=" C   ARG A 129 "
       model="   0" pdb=" N   SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.015 1.40e-02 5.10e+03 1.09e+00
  bond model="   0" pdb=" C   PRO A 114 "
       model="   0" pdb=" N   ALA A 115 "
    ideal  model  delta    sigma   weight residual
    1.329  1.315  0.014 1.40e-02 5.10e+03 1.07e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.08 -   106.26: 47
      106.26 -   112.44: 2704
      112.44 -   118.62: 447
      118.62 -   124.80: 839
      124.80 -   130.99: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  124.17   -6.17 3.00e+00 1.11e-01 4.23e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  114.36   -5.36 3.00e+00 1.11e-01 3.19e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.77    5.23 3.00e+00 1.11e-01 3.04e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.95   -4.95 3.00e+00 1.11e-01 2.73e+00
  angle model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" CB  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     111.60  108.62    2.98 2.00e+00 2.50e-01 2.22e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.89: 993
       14.89 -    29.78: 21
       29.78 -    44.67: 13
       44.67 -    59.56: 4
       59.56 -    74.45: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   66.11  -66.11     1      3.00e+01 1.11e-03 6.35e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   74.45  -74.45     2      3.00e+01 1.11e-03 4.95e+00
  dihedral model="   0" pdb=" CE1 TYR A  91 "
           model="   0" pdb=" CZ  TYR A  91 "
           model="   0" pdb=" OH  TYR A  91 "
           model="   0" pdb=" HH  TYR A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -56.11   56.11     2      3.00e+01 1.11e-03 3.67e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 104
       0.028 -    0.057: 55
       0.057 -    0.085: 3
       0.085 -    0.113: 11
       0.113 -    0.142: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 5.01e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.24e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.014 5.00e-02 4.00e+02   2.14e-02 7.32e-01
        model="   0" pdb=" N   PRO A   6 "    0.037 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.011 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.012 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.008 2.00e-02 2.50e+03   4.35e-03 5.66e-01
        model="   0" pdb=" CG  TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 138 "    0.007 2.00e-02 2.50e+03   4.81e-03 4.64e-01
        model="   0" pdb=" CG  HIS A 138 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 138 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 138 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 138 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 138 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 138 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 138 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     1.98: 24
        1.98 -     2.64: 2817
        2.64 -     3.29: 6624
        3.29 -     3.95: 7938
        3.95 -     4.60: 12226
  Nonbonded interactions: 29629
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 LEU A 119 "
            model="   0" pdb=" O   ILE A 122 "
     model   vdw
     1.329 2.620
  nonbonded model="   0" pdb=" HB2 ASP A 118 "
            model="   0" pdb=" HE3 LYS A 125 "
     model   vdw
     1.690 2.440
  nonbonded model="   0" pdb=" HE1 TYR A  89 "
            model="   0" pdb=" HH  TYR A  91 "
     model   vdw
     1.708 2.100
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" HB2 ASP A  44 "
     model   vdw
     1.728 2.440
  nonbonded model="   0" pdb=" HG2 LYS A 113 "
            model="   0" pdb=" HE3 MET A 128 "
     model   vdw
     1.739 2.440
  ... (remaining 29624 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: 105
        1.23 -     1.43: 367
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.62e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.07e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.84e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.56e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.36e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.55 -   106.18: 103
      106.18 -   111.82: 2493
      111.82 -   117.45: 476
      117.45 -   123.08: 781
      123.08 -   128.71: 226
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.76    3.84 1.00e+00 1.00e+00 1.48e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.34   -3.74 1.00e+00 1.00e+00 1.40e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
      ideal   model   delta    sigma   weight residual
     116.20  123.54   -7.34 2.00e+00 2.50e-01 1.35e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.14    3.46 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.93   -3.33 1.00e+00 1.00e+00 1.11e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 968
       17.43 -    34.86: 47
       34.86 -    52.29: 14
       52.29 -    69.72: 3
       69.72 -    87.15: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A  43 "
           model="   0" pdb=" C   HIS A  43 "
           model="   0" pdb=" N   ASP A  44 "
           model="   0" pdb=" CA  ASP A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.93   20.07     0      5.00e+00 4.00e-02 1.61e+01
  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  160.19   19.81     0      5.00e+00 4.00e-02 1.57e+01
  dihedral model="   0" pdb=" CA  MET A 128 "
           model="   0" pdb=" C   MET A 128 "
           model="   0" pdb=" N   ARG A 129 "
           model="   0" pdb=" CA  ARG A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.03   18.97     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 86
       0.052 -    0.104: 56
       0.104 -    0.156: 30
       0.156 -    0.208: 3
       0.208 -    0.260: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality model="   0" pdb=" CG  LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
            model="   0" pdb=" CD1 LEU A  93 "
            model="   0" pdb=" CD2 LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality model="   0" pdb=" CA  ALA A 115 "
            model="   0" pdb=" N   ALA A 115 "
            model="   0" pdb=" C   ALA A 115 "
            model="   0" pdb=" CB  ALA A 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.65   -0.17 2.00e-01 2.50e+01 6.88e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.084 2.00e-02 2.50e+03   3.49e-02 3.65e+01
        model="   0" pdb=" CG  TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A  43 "   -0.071 2.00e-02 2.50e+03   4.27e-02 3.64e+01
        model="   0" pdb=" CG  HIS A  43 "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 "    0.067 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 "   -0.036 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.048 2.00e-02 2.50e+03   1.85e-02 1.02e+01
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 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 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 147
        2.19 -     2.80: 4320
        2.80 -     3.40: 5879
        3.40 -     4.00: 7087
        4.00 -     4.60: 10757
  Nonbonded interactions: 28190
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE1 PHE A  67 "
            model="   0" pdb="HD23 LEU A  99 "
     model   vdw
     1.592 2.270
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.731 1.850
  nonbonded model="   0" pdb=" O   ASP A 118 "
            model="   0" pdb=" H   ILE A 122 "
     model   vdw
     1.756 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.761 1.850
  nonbonded model="   0" pdb=" HG1 THR A  82 "
            model="   0" pdb=" O   ASP A  88 "
     model   vdw
     1.765 1.850
  ... (remaining 28185 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: 0.83, per 1000 atoms: 0.37
  Number of scatterers: 2224
  At special positions: 0
  Unit cell: (55.537, 43.618, 57.481, 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     216      8.00
     N     180      7.00
     C     713      6.00
     H    1113      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: 0.80
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.88 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: 394
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.24e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.90e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.56e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.97e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 5.89e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.94 -   105.70: 59
      105.70 -   111.46: 2424
      111.46 -   117.22: 573
      117.22 -   122.98: 781
      122.98 -   128.74: 242
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.83    3.77 1.00e+00 1.00e+00 1.42e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.30    4.90 1.30e+00 5.92e-01 1.42e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.34    4.86 1.30e+00 5.92e-01 1.40e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.93    3.67 1.00e+00 1.00e+00 1.35e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.07   -3.47 1.00e+00 1.00e+00 1.20e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 980
       16.97 -    33.94: 31
       33.94 -    50.91: 18
       50.91 -    67.88: 2
       67.88 -    84.85: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.60   17.40     0      5.00e+00 4.00e-02 1.21e+01
  dihedral model="   0" pdb=" CG  ARG A 129 "
           model="   0" pdb=" CD  ARG A 129 "
           model="   0" pdb=" NE  ARG A 129 "
           model="   0" pdb=" CZ  ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -141.57  -38.43     2      1.50e+01 4.44e-03 8.24e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.039: 83
       0.039 -    0.078: 38
       0.078 -    0.117: 33
       0.117 -    0.155: 19
       0.155 -    0.194: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.42e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.21e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.43e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.052 2.00e-02 2.50e+03   2.16e-02 1.40e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 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 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.018 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 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.051 2.00e-02 2.50e+03   1.98e-02 1.18e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "    0.038 2.00e-02 2.50e+03   1.73e-02 8.96e+00
        model="   0" pdb=" CG  TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 140
        2.18 -     2.79: 4267
        2.79 -     3.39: 6062
        3.39 -     4.00: 7469
        4.00 -     4.60: 11337
  Nonbonded interactions: 29275
  Sorted by model distance:
  nonbonded model="   0" pdb="HG23 THR A  82 "
            model="   0" pdb=" HB3 SER A  90 "
     model   vdw
     1.577 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.713 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  44 "
            model="   0" pdb=" HZ1 LYS A 125 "
     model   vdw
     1.770 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.775 1.850
  ... (remaining 29270 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}
  Time building chain proxies: 0.95, per 1000 atoms: 0.43
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.599, 64.33, 52.973, 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      : 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=  2.966)
  Mean delta:    0.012 (Z=  0.637)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   134.70   -13.00  1.80e+00  5.22e+01   7.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.32     4.28  1.00e+00  1.83e+01   4.3*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  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:   13.005 (Z=  7.225)
  Mean delta:    1.677 (Z=  0.922)

                      ----------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   152.37    27.63  5.00e+00  3.05e+01   5.5*sigma

  Min. delta:    0.014
  Max. delta:   85.167
  Mean delta:   12.685

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:    0.221
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.074
  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----------                   

    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 

============================ 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= 0.454
    Angle     :  1.586  13.005   4079  Z= 0.694
    Chirality :  0.076   0.221    176
    Planarity :  0.008   0.056    327
    Dihedral  : 11.303  85.167    769
    Min Nonbonded Distance : 1.635
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  3.65 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.84 %
      Favored  : 92.74 %
    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:  0.44 (0.72), residues: 137
    helix:  0.42 (0.53), residues: 81
    sheet: -2.61 (1.27), residues: 10
    loop :  1.17 (1.08), residues: 46
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 136 
   PHE   0.023   0.004   PHE A  45 
   TYR   0.061   0.011   TYR A 111 
   ARG   0.060   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 136 
   PHE   0.013   0.004   PHE A  45 
   TYR   0.050   0.013   TYR A 111 
   ARG   0.006   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: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  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: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 seconds

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

  Ramachandran outliers =   2.19 %
                favored =  94.16 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   1.35
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.59
  MolProbity score      =   1.55

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: 72
        1.23 -     1.43: 400
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.84e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.99e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.25e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.94e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.89e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.15 -   105.86: 79
      105.86 -   111.58: 2441
      111.58 -   117.29: 538
      117.29 -   123.01: 794
      123.01 -   128.72: 227
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.42    4.18 1.00e+00 1.00e+00 1.75e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.84    3.76 1.00e+00 1.00e+00 1.41e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.01    3.59 1.00e+00 1.00e+00 1.29e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.04   -3.44 1.00e+00 1.00e+00 1.18e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.82    4.38 1.30e+00 5.92e-01 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 962
       16.65 -    33.30: 52
       33.30 -    49.95: 12
       49.95 -    66.60: 4
       66.60 -    83.25: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.66   22.34     0      5.00e+00 4.00e-02 2.00e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.23  -21.77     0      5.00e+00 4.00e-02 1.90e+01
  dihedral model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" C   HIS A 137 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.80   21.20     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 80
       0.050 -    0.100: 59
       0.100 -    0.149: 30
       0.149 -    0.199: 6
       0.199 -    0.249: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 135 "
            model="   0" pdb=" N   HIS A 135 "
            model="   0" pdb=" C   HIS A 135 "
            model="   0" pdb=" CB  HIS A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" C   THR A  82 "
            model="   0" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.19 2.00e-01 2.50e+01 9.30e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.26e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.049 2.00e-02 2.50e+03   2.47e-02 1.84e+01
        model="   0" pdb=" CG  TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.019 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 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.048 2.00e-02 2.50e+03   2.08e-02 1.29e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.010 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 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.052 2.00e-02 2.50e+03   2.01e-02 1.21e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.05 -     1.76: 6
        1.76 -     2.47: 1427
        2.47 -     3.18: 6712
        3.18 -     3.89: 7971
        3.89 -     4.60: 12318
  Nonbonded interactions: 28434
  Sorted by model distance:
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb="HH21 ARG A 127 "
     model   vdw
     1.052 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.581 1.850
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.598 1.850
  nonbonded model="   0" pdb="HD22 LEU A 119 "
            model="   0" pdb="HD11 ILE A 122 "
     model   vdw
     1.667 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.703 1.850
  ... (remaining 28429 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: 63
        1.23 -     1.43: 409
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.81e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.80e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.76e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.68e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.56e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.93 -   105.79: 67
      105.79 -   111.65: 2490
      111.65 -   117.51: 515
      117.51 -   123.37: 837
      123.37 -   129.22: 170
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.62    3.98 1.00e+00 1.00e+00 1.58e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.22   -4.82 1.40e+00 5.10e-01 1.19e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.00   -3.40 1.00e+00 1.00e+00 1.16e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.87    4.33 1.30e+00 5.92e-01 1.11e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.40    3.20 1.00e+00 1.00e+00 1.03e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 978
       17.62 -    35.23: 44
       35.23 -    52.85: 9
       52.85 -    70.46: 1
       70.46 -    88.08: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A 113 "
           model="   0" pdb=" C   LYS A 113 "
           model="   0" pdb=" N   PRO A 114 "
           model="   0" pdb=" CA  PRO A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" CB  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.86    7.26     0      2.50e+00 1.60e-01 8.44e+00
  dihedral model="   0" pdb=" CB  MET A   1 "
           model="   0" pdb=" CG  MET A   1 "
           model="   0" pdb=" SD  MET A   1 "
           model="   0" pdb=" CE  MET A   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -133.87  -46.13     3      1.50e+01 4.44e-03 8.28e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 84
       0.045 -    0.090: 44
       0.090 -    0.135: 39
       0.135 -    0.180: 7
       0.180 -    0.225: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.40e-01
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.50e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.057 2.00e-02 2.50e+03   2.34e-02 1.64e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.057 2.00e-02 2.50e+03   2.24e-02 1.51e+01
        model="   0" pdb=" CG  TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.006 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 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.015 2.00e-02 2.50e+03   3.10e-02 9.63e+00
        model="   0" pdb=" CG  ASP A  36 "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.018 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 118
        2.18 -     2.79: 4238
        2.79 -     3.39: 5904
        3.39 -     4.00: 7262
        4.00 -     4.60: 10796
  Nonbonded interactions: 28318
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.577 1.850
  nonbonded model="   0" pdb=" HB3 HIS A  43 "
            model="   0" pdb=" HE3 LYS A 113 "
     model   vdw
     1.662 2.440
  nonbonded model="   0" pdb="HG23 THR A  82 "
            model="   0" pdb=" HB3 SER A  90 "
     model   vdw
     1.683 2.440
  nonbonded model="   0" pdb=" HE2 LYS A  79 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.690 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.693 1.850
  ... (remaining 28313 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: 0.87
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.97 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: (43.978, 55.847, 53.369, 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: 93
        1.23 -     1.43: 379
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.13e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.11e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.09e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.59e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 5.13e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.83 -   106.46: 122
      106.46 -   112.08: 2513
      112.08 -   117.70: 442
      117.70 -   123.32: 834
      123.32 -   128.94: 168
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.71    3.89 1.00e+00 1.00e+00 1.52e+01
  angle model="   0" pdb=" C   GLU A 120 "
        model="   0" pdb=" N   GLY A 121 "
        model="   0" pdb=" CA  GLY A 121 "
      ideal   model   delta    sigma   weight residual
     121.70  128.18   -6.48 1.80e+00 3.09e-01 1.30e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.59    4.61 1.30e+00 5.92e-01 1.26e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.12    3.48 1.00e+00 1.00e+00 1.21e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.88    4.32 1.30e+00 5.92e-01 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 985
       17.44 -    34.87: 36
       34.87 -    52.31: 9
       52.31 -    69.74: 2
       69.74 -    87.18: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A 120 "
           model="   0" pdb=" C   GLU A 120 "
           model="   0" pdb=" N   GLY A 121 "
           model="   0" pdb=" CA  GLY A 121 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.84   32.16     0      5.00e+00 4.00e-02 4.14e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.47   18.53     0      5.00e+00 4.00e-02 1.37e+01
  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  164.50   15.50     0      5.00e+00 4.00e-02 9.62e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 82
       0.043 -    0.086: 46
       0.086 -    0.129: 34
       0.129 -    0.172: 12
       0.172 -    0.215: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.28e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.28e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.057 2.00e-02 2.50e+03   2.24e-02 1.51e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "    0.045 2.00e-02 2.50e+03   2.07e-02 1.28e+01
        model="   0" pdb=" CG  TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "   -0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.052 2.00e-02 2.50e+03   1.99e-02 1.19e+01
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 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 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.017 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 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.36 -     2.01: 29
        2.01 -     2.66: 2913
        2.66 -     3.31: 6546
        3.31 -     3.95: 7738
        3.95 -     4.60: 11802
  Nonbonded interactions: 29028
  Sorted by model distance:
  nonbonded model="   0" pdb=" HG1 THR A  82 "
            model="   0" pdb=" O   ASP A  88 "
     model   vdw
     1.365 1.850
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.464 1.850
  nonbonded model="   0" pdb="HD13 LEU A  39 "
            model="   0" pdb=" HG2 LYS A 125 "
     model   vdw
     1.638 2.440
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.647 1.850
  nonbonded model="   0" pdb=" OH  TYR A  68 "
            model="   0" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.691 1.850
  ... (remaining 29023 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: 0.75 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: 72
        1.23 -     1.43: 400
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.88e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.88e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.74e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.46e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.44e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.06 -   105.88: 76
      105.88 -   111.69: 2471
      111.69 -   117.51: 520
      117.51 -   123.32: 836
      123.32 -   129.14: 176
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.17   -3.57 1.00e+00 1.00e+00 1.27e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.04    3.56 1.00e+00 1.00e+00 1.27e+01
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  128.09   -6.39 1.80e+00 3.09e-01 1.26e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.14   -4.74 1.40e+00 5.10e-01 1.15e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.81    4.39 1.30e+00 5.92e-01 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 966
       16.85 -    33.69: 47
       33.69 -    50.54: 14
       50.54 -    67.39: 4
       67.39 -    84.23: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.04   34.96     0      5.00e+00 4.00e-02 4.89e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.94   27.06     0      5.00e+00 4.00e-02 2.93e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.69   24.31     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.042: 76
       0.042 -    0.083: 48
       0.083 -    0.125: 34
       0.125 -    0.166: 15
       0.166 -    0.207: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.35e-01
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.00e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.064 2.00e-02 2.50e+03   2.81e-02 2.38e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 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 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.021 2.00e-02 2.50e+03   4.27e-02 1.82e+01
        model="   0" pdb=" CG  ASP A  36 "    0.074 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.053 2.00e-02 2.50e+03   2.09e-02 1.30e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 187
        2.23 -     2.82: 4545
        2.82 -     3.41: 5896
        3.41 -     4.01: 7206
        4.01 -     4.60: 10902
  Nonbonded interactions: 28736
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.632 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.700 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.701 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" HB  THR A  82 "
            model="   0" pdb=" HG3 GLU A  84 "
     model   vdw
     1.731 2.440
  ... (remaining 28731 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: 0.62
  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.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 58
        1.23 -     1.42: 414
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.19e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.65e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.03e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.91e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.60e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.32 -   106.03: 94
      106.03 -   111.74: 2466
      111.74 -   117.44: 505
      117.44 -   123.15: 799
      123.15 -   128.86: 215
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  128.64   -6.94 1.80e+00 3.09e-01 1.49e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.07    3.53 1.00e+00 1.00e+00 1.25e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.89    4.31 1.30e+00 5.92e-01 1.10e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.86   -3.26 1.00e+00 1.00e+00 1.06e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.86   -4.46 1.40e+00 5.10e-01 1.01e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 976
       16.91 -    33.82: 39
       33.82 -    50.74: 12
       50.74 -    67.65: 4
       67.65 -    84.56: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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  156.30   23.70     0      5.00e+00 4.00e-02 2.25e+01
  dihedral model="   0" pdb=" CA  HIS A 134 "
           model="   0" pdb=" C   HIS A 134 "
           model="   0" pdb=" N   HIS A 135 "
           model="   0" pdb=" CA  HIS A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.39   16.61     0      5.00e+00 4.00e-02 1.10e+01
  dihedral model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" C   HIS A 137 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.91   16.09     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 67
       0.036 -    0.071: 43
       0.071 -    0.107: 39
       0.107 -    0.143: 21
       0.143 -    0.178: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.94e-01
  chirality model="   0" pdb=" CA  HIS A 134 "
            model="   0" pdb=" N   HIS A 134 "
            model="   0" pdb=" C   HIS A 134 "
            model="   0" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.67e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.58e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.062 2.00e-02 2.50e+03   2.52e-02 1.91e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.050 2.00e-02 2.50e+03   1.95e-02 1.14e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.016 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 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A 118 "   -0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        model="   0" pdb=" CG  ASP A 118 "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A 118 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A 118 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 183
        2.21 -     2.81: 4431
        2.81 -     3.41: 5890
        3.41 -     4.00: 7147
        4.00 -     4.60: 10762
  Nonbonded interactions: 28413
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.617 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.618 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  49 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.705 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.731 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.735 1.850
  ... (remaining 28408 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: 0.74
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.87 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: 96
        1.23 -     1.43: 376
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.16e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.54e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.73e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.62e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.56e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.55 -   105.37: 37
      105.37 -   111.19: 2385
      111.19 -   117.01: 639
      117.01 -   122.83: 736
      122.83 -   128.65: 282
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.61    3.99 1.00e+00 1.00e+00 1.60e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.49   -3.89 1.00e+00 1.00e+00 1.51e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.44    4.76 1.30e+00 5.92e-01 1.34e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  119.00    3.60 1.00e+00 1.00e+00 1.29e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.55    4.65 1.30e+00 5.92e-01 1.28e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 990
       17.48 -    34.95: 26
       34.95 -    52.43: 11
       52.43 -    69.91: 3
       69.91 -    87.38: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  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  157.59   22.41     0      5.00e+00 4.00e-02 2.01e+01
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.62   17.38     0      5.00e+00 4.00e-02 1.21e+01
  dihedral model="   0" pdb=" CG  ARG A 129 "
           model="   0" pdb=" CD  ARG A 129 "
           model="   0" pdb=" NE  ARG A 129 "
           model="   0" pdb=" CZ  ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  130.90  -40.90     2      1.50e+01 4.44e-03 9.14e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 85
       0.037 -    0.073: 35
       0.073 -    0.110: 29
       0.110 -    0.146: 22
       0.146 -    0.183: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.34e-01
  chirality model="   0" pdb=" CA  GLU A  49 "
            model="   0" pdb=" N   GLU A  49 "
            model="   0" pdb=" C   GLU A  49 "
            model="   0" pdb=" CB  GLU A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.39e-01
  chirality model="   0" pdb=" CG  LEU A 132 "
            model="   0" pdb=" CB  LEU A 132 "
            model="   0" pdb=" CD1 LEU A 132 "
            model="   0" pdb=" CD2 LEU A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.88e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.049 2.00e-02 2.50e+03   1.87e-02 1.05e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.015 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 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.045 2.00e-02 2.50e+03   1.76e-02 9.30e+00
        model="   0" pdb=" CG  TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.037 2.00e-02 2.50e+03   1.48e-02 6.58e+00
        model="   0" pdb=" CG  TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.18 -     1.87: 9
        1.87 -     2.55: 1863
        2.55 -     3.23: 6669
        3.23 -     3.92: 7893
        3.92 -     4.60: 11970
  Nonbonded interactions: 28404
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ILE A  51 "
            model="   0" pdb=" HG  SER A 130 "
     model   vdw
     1.184 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.594 1.850
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.599 1.850
  nonbonded model="   0" pdb=" OH  TYR A  68 "
            model="   0" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.755 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.772 1.850
  ... (remaining 28399 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: 0.96
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.08 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: 1113
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2248
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" 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="   0" pdb=" NE  ARG A 129 "
       model="   0" 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="   0" pdb=" NE  ARG A 127 "
       model="   0" 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="   0" pdb=" CZ  ARG A 127 "
       model="   0" 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="   0" pdb=" CZ  ARG A  21 "
       model="   0" 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 2243 not shown)

  Histogram of bond angle deviations from ideal:
       34.59 -    53.85: 1
       53.85 -    73.11: 0
       73.11 -    92.38: 0
       92.38 -   111.64: 2723
      111.64 -   130.91: 1367
  Bond angle restraints: 4091
  Sorted by residual:
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H3  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47   34.59   74.88 3.00e+00 1.11e-01 6.23e+02
  angle model="   0" pdb=" H1  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H2  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  126.39  -16.92 3.00e+00 1.11e-01 3.18e+01
  angle model="   0" pdb=" CA  MET A   1 "
        model="   0" pdb=" N   MET A   1 "
        model="   0" pdb=" H1  MET A   1 "
      ideal   model   delta    sigma   weight residual
     109.47  119.15   -9.68 3.00e+00 1.11e-01 1.04e+01
  angle model="   0" pdb=" CA  GLY A  96 "
        model="   0" pdb=" N   GLY A  96 "
        model="   0" pdb=" H   GLY A  96 "
      ideal   model   delta    sigma   weight residual
     114.00  119.96   -5.96 3.00e+00 1.11e-01 3.95e+00
  angle model="   0" pdb=" CA  GLY A  87 "
        model="   0" pdb=" N   GLY A  87 "
        model="   0" pdb=" H   GLY A  87 "
      ideal   model   delta    sigma   weight residual
     114.00  119.91   -5.91 3.00e+00 1.11e-01 3.89e+00
  ... (remaining 4086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 814
       17.66 -    35.33: 93
       35.33 -    52.99: 87
       52.99 -    70.65: 37
       70.65 -    88.32: 8
  Dihedral angle restraints: 1039
    sinusoidal: 561
      harmonic: 478
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A 120 "
           model="   0" pdb=" CG  GLU A 120 "
           model="   0" pdb=" CD  GLU A 120 "
           model="   0" 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="   0" pdb=" CB  GLU A  24 "
           model="   0" pdb=" CG  GLU A  24 "
           model="   0" pdb=" CD  GLU A  24 "
           model="   0" 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="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" CB  ASP A 116 "
           model="   0" pdb=" CG  ASP A 116 "
           model="   0" 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 1036 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="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" 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="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" 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="   0" pdb=" CA  ILE A  71 "
            model="   0" pdb=" N   ILE A  71 "
            model="   0" pdb=" C   ILE A  71 "
            model="   0" 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="   0" pdb=" CB  TYR A  91 "   -0.001 2.00e-02 2.50e+03   6.41e-04 1.23e-02
        model="   0" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "   -0.001 2.00e-02 2.50e+03   5.48e-04 9.01e-03
        model="   0" pdb=" CG  PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.000 2.00e-02 2.50e+03   5.02e-04 7.55e-03
        model="   0" pdb=" CG  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.46: 1393
        2.46 -     3.00: 5157
        3.00 -     3.53: 5460
        3.53 -     4.07: 6879
        4.07 -     4.60: 9626
  Nonbonded interactions: 28515
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LEU A   9 "
            model="   0" pdb=" H   SER A  13 "
     model   vdw
     1.926 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" H   SER A  65 "
     model   vdw
     1.929 1.850
  nonbonded model="   0" pdb=" O   LYS A  27 "
            model="   0" pdb=" H   LEU A  31 "
     model   vdw
     1.934 1.850
  nonbonded model="   0" pdb=" O   THR A  56 "
            model="   0" pdb=" H   ALA A  60 "
     model   vdw
     1.955 1.850
  nonbonded model="   0" pdb=" H   LEU A   3 "
            model="   0" pdb=" H   ILE A   4 "
     model   vdw
     1.975 2.100
  ... (remaining 28510 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: 0.98
  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.

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: 44
        1.23 -     1.42: 428
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.42e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.08e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.80e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.22e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.08e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.98 -   105.74: 69
      105.74 -   111.49: 2409
      111.49 -   117.25: 575
      117.25 -   123.00: 790
      123.00 -   128.76: 236
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.49    4.11 1.00e+00 1.00e+00 1.69e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.27   -3.67 1.00e+00 1.00e+00 1.34e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  119.06    3.54 1.00e+00 1.00e+00 1.25e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.61    4.59 1.30e+00 5.92e-01 1.25e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" 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
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.22: 958
       16.22 -    32.45: 54
       32.45 -    48.67: 17
       48.67 -    64.90: 2
       64.90 -    81.12: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.64  -27.36     0      5.00e+00 4.00e-02 2.99e+01
  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  158.00   22.00     0      5.00e+00 4.00e-02 1.94e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.88  -21.12     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 74
       0.046 -    0.090: 52
       0.090 -    0.135: 36
       0.135 -    0.179: 10
       0.179 -    0.224: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    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="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    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="   0" pdb=" CB  TYR A  50 "    0.075 2.00e-02 2.50e+03   3.18e-02 3.04e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.063 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 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.020 2.00e-02 2.50e+03   4.13e-02 1.70e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.071 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.024 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.058 2.00e-02 2.50e+03   2.22e-02 1.48e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 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 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.10: 67
        2.10 -     2.73: 3648
        2.73 -     3.35: 6181
        3.35 -     3.98: 7454
        3.98 -     4.60: 11166
  Nonbonded interactions: 28516
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.476 2.440
  nonbonded model="   0" pdb=" OD1 ASN A  72 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.509 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.596 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.677 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.680 1.850
  ... (remaining 28511 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: 1.10 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: 1
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.335 -0.014 1.00e-02 1.00e+04 1.90e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.334 -0.013 1.00e-02 1.00e+04 1.78e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.48e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.47e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.315  0.015 1.30e-02 5.92e+03 1.36e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.01 -   106.20: 41
      106.20 -   112.39: 2703
      112.39 -   118.59: 445
      118.59 -   124.78: 847
      124.78 -   130.97: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  123.59   -5.59 3.00e+00 1.11e-01 3.48e+00
  angle model="   0" pdb=" N   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     110.00  115.25   -5.25 3.00e+00 1.11e-01 3.06e+00
  angle model="   0" pdb=" N   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" C   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     112.10  107.86    4.24 2.50e+00 1.60e-01 2.87e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  104.10    4.90 3.00e+00 1.11e-01 2.66e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  104.19    4.81 3.00e+00 1.11e-01 2.57e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 991
       16.00 -    32.00: 24
       32.00 -    48.01: 9
       48.01 -    64.01: 6
       64.01 -    80.01: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -80.01   80.01     1      3.00e+01 1.11e-03 8.82e+00
  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  166.91   13.09     0      5.00e+00 4.00e-02 6.85e+00
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   68.26  -68.26     1      3.00e+01 1.11e-03 6.72e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 124
       0.030 -    0.059: 38
       0.059 -    0.088: 3
       0.088 -    0.117: 8
       0.117 -    0.147: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.38e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.67e-01
  chirality model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.015 5.00e-02 4.00e+02   2.27e-02 8.23e-01
        model="   0" pdb=" N   PRO A   6 "   -0.039 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.013 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.001 2.00e-02 2.50e+03   3.79e-03 4.31e-01
        model="   0" pdb=" CG  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.004 2.00e-02 2.50e+03   3.50e-03 3.68e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 321
        2.29 -     2.87: 5153
        2.87 -     3.44: 5435
        3.44 -     4.02: 7293
        4.02 -     4.60: 10777
  Nonbonded interactions: 28979
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   VAL A  41 "
            model="   0" pdb=" H   LYS A 113 "
     model   vdw
     1.710 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.721 1.850
  nonbonded model="   0" pdb=" OH  TYR A  68 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.742 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.768 1.850
  nonbonded model="   0" pdb=" HE1 PHE A  67 "
            model="   0" pdb=" HG  LEU A  99 "
     model   vdw
     1.772 2.270
  ... (remaining 28974 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:    0.021 (Z=  1.509)
  Mean delta:    0.004 (Z=  0.261)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.261 (Z=  2.236)
  Mean delta:    0.849 (Z=  0.380)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   80.949
  Mean delta:   12.628

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.213
  Mean delta:    0.057

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.029
  Mean delta:    0.003

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.021   2242  Z= 0.186
    Angle     :  1.168   6.261   4079  Z= 0.419
    Chirality :  0.057   0.213    176
    Planarity :  0.003   0.029    327
    Dihedral  : 11.524  89.040    769
    Min Nonbonded Distance : 1.452
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.81 %
      Favored  : 99.19 %
    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:  1.46 (0.68), residues: 137
    helix:  0.25 (0.61), residues: 63
    sheet:  None (None), residues: 0
    loop :  1.96 (0.70), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 135 
   PHE   0.005   0.002   PHE A  15 
   TYR   0.021   0.003   TYR A 111 
   ARG   0.006   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 135 
   PHE   0.004   0.001   PHE A  45 
   TYR   0.019   0.004   TYR A 111 
   ARG   0.002   0.001   ARG A 127 

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

   A 139  HIS

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

  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   4.51
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.17
  MolProbity score      =   1.23

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:    0.038 (Z=  2.728)
  Mean delta:    0.012 (Z=  0.600)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.58     4.02  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.256 (Z=  4.017)
  Mean delta:    1.589 (Z=  0.862)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   87.054
  Mean delta:   11.767

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.250
  Mean delta:    0.077

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.065
  Mean delta:    0.010

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.427
    Angle     :  1.527   7.256   4079  Z= 0.658
    Chirality :  0.077   0.250    176
    Planarity :  0.008   0.048    327
    Dihedral  : 10.759  87.054    769
    Min Nonbonded Distance : 1.719
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  1.61 %
      Favored  : 98.39 %
    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:  0.89 (0.70), residues: 137
    helix:  0.56 (0.52), residues: 81
    sheet: -2.67 (1.15), residues: 12
    loop :  2.15 (1.06), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.065   0.007   TYR A 111 
   ARG   0.052   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.008   0.004   PHE A  45 
   TYR   0.054   0.008   TYR A 111 
   ARG   0.006   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   2.71
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.53
  MolProbity score      =   1.10

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 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  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: "   0"
    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)----------                  


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:    0.038 (Z=  2.666)
  Mean delta:    0.011 (Z=  0.591)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   132.11   -10.41  1.80e+00  3.34e+01   5.8*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   10.662 (Z=  5.784)
  Mean delta:    1.663 (Z=  0.901)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00  -151.26   -28.74  5.00e+00  3.30e+01   5.7*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -155.19   -24.81  5.00e+00  2.46e+01   5.0*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 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   159.72    20.28  5.00e+00  1.64e+01   4.1*sigma

  Min. delta:    0.006
  Max. delta:   84.169
  Mean delta:   13.652

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.441
  Mean delta:    0.085

                       ----------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            0.086       0.155      147.22   7.8*sigma

  Min. delta:    0.000
  Max. delta:    0.086
  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----------                   

    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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.421
    Angle     :  1.583  10.907   4079  Z= 0.685
    Chirality :  0.085   0.441    176
    Planarity :  0.009   0.081    327
    Dihedral  : 11.854  84.169    769
    Min Nonbonded Distance : 1.732
  
  Molprobity Statistics.
    All-atom Clashscore : 9.02
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  3.23 %
      Favored  : 92.74 %
    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: -0.87 (0.67), residues: 137
    helix:  0.45 (0.53), residues: 82
    sheet:  None (None), residues: 0
    loop : -2.20 (0.80), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.032   0.007   PHE A  67 
   TYR   0.191   0.016   TYR A 111 
   ARG   0.036   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.020   0.007   PHE A  67 
   TYR   0.155   0.019   TYR A 111 
   ARG   0.005   0.002   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: {'PTRANS': 7, 'TRANS': 131}
  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   9.02
  RMS(bonds)            =   0.0081
  RMS(angles)           =   1.58
  MolProbity score      =   2.30

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=  2.599)
  Mean delta:    0.012 (Z=  0.618)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.055 (Z=  3.948)
  Mean delta:    1.560 (Z=  0.856)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   79.041
  Mean delta:   10.689

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.189
  Mean delta:    0.073

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.051
  Mean delta:    0.011

============================= 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 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.440
    Angle     :  1.508   6.055   4079  Z= 0.654
    Chirality :  0.073   0.189    176
    Planarity :  0.008   0.049    327
    Dihedral  :  9.980  79.041    769
    Min Nonbonded Distance : 1.563
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.00 %
      Favored  : 98.39 %
    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:  1.08 (0.72), residues: 137
    helix:  0.46 (0.51), residues: 85
    sheet: -2.78 (1.07), residues: 12
    loop :  3.11 (1.16), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 137 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.062   0.010   TYR A 111 
   ARG   0.041   0.011   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 137 
   PHE   0.007   0.003   PHE A  45 
   TYR   0.052   0.012   TYR A 111 
   ARG   0.006   0.002   ARG A  21 

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

   A 134  HIS
   A  66  GLN

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

  Time building chain proxies: 1.06, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.802, 74.153, 45.522, 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 =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.51
  MolProbity score      =   1.52

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