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


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


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

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

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

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

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


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

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

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


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


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


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

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

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

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

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


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


  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: ""

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

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

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

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

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

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


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

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

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


============================== 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 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 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 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: ""

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

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

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

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}
  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.759, 46.159, 63.023, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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}
        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: 0.71, per 1000 atoms: 0.32
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.767, 71.48, 41.612, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 0.61, per 1000 atoms: 0.28
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.788, 53.985, 47.289, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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}

  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)----------                  

  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.546, 43.162, 71.508, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: (59.502, 54.312, 69.949, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: ""

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

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

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

  Time building chain proxies: 1.20, per 1000 atoms: 0.54
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (68.048, 57.499, 51.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: ""

  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: ""

  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: "   1"
    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: (43.013, 69.391, 55.745, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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 ==============================


  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: ""

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


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   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}

  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: 0.67
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.76 seconds

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

        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: 0.60
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.68 seconds

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

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

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 55
        1.23 -     1.42: 417
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.67e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.61e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    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=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.01e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.89e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.85 -   105.72: 82
      105.72 -   111.59: 2401
      111.59 -   117.47: 581
      117.47 -   123.34: 841
      123.34 -   129.21: 174
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.32    4.88 1.30e+00 5.92e-01 1.41e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.35    4.85 1.30e+00 5.92e-01 1.39e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" N   ILE A  86 " segid="A   "
        model="   0" pdb=" CA  ILE A  86 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.70  128.09   -6.39 1.80e+00 3.09e-01 1.26e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 958
       15.98 -    31.97: 45
       31.97 -    47.95: 21
       47.95 -    63.94: 6
       63.94 -    79.92: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.12   15.88     0      5.00e+00 4.00e-02 1.01e+01
  dihedral model="   0" pdb=" N   HIS A 137 " segid="A   "
           model="   0" pdb=" CA  HIS A 137 " segid="A   "
           model="   0" pdb=" CB  HIS A 137 " segid="A   "
           model="   0" pdb=" CG  HIS A 137 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.69   58.69     3      1.50e+01 4.44e-03 9.47e+00
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.17    7.57     0      2.50e+00 1.60e-01 9.18e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.050: 79
       0.050 -    0.098: 52
       0.098 -    0.147: 36
       0.147 -    0.196: 7
       0.196 -    0.245: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    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=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    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  50 " segid="A   "   -0.044 2.00e-02 2.50e+03   4.81e-02 6.93e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.124 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.075 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.031 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.088 2.00e-02 2.50e+03   3.45e-02 3.58e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane mo
  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 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: ""
del="   0" pdb=" CB  TYR A 111 " segid="A   "    0.057 2.00e-02 2.50e+03   3.15e-02 2.97e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.027 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 312
        2.29 -     2.87: 5115
        2.87 -     3.45: 5525
        3.45 -     4.02: 7276
        4.02 -     4.60: 10662
  Nonbonded interactions: 28890
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.714 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.795 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.802 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.808 1.850
  ... (remaining 28885 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49, 50.721, 58.223, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 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=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.26e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.87e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.68e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.27e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.20e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.67 -   105.60: 73
      105.60 -   111.53: 2396
      111.53 -   117.46: 592
      117.46 -   123.38: 840
      123.38 -   129.31: 178
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.78    4.82 1.00e+00 1.00e+00 2.32e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" CA  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.58   -3.98 1.00e+00 1.00e+00 1.58e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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 138 " segid="A   "
        model="   0" pdb=" CG  HIS A 138 " segid="A   "
        model="   0" pdb=" CD2 HIS A 138 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.31    4.89 1.30e+00 5.92e-01 1.42e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.63: 948
       15.63 -    31.25: 59
       31.25 -    46.88: 19
       46.88 -    62.51: 5
       62.51 -    78.13: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.33   39.67     0      5.00e+00 4.00e-02 6.29e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.34   15.66     0      5.00e+00 4.00e-02 9.81e+00
  dihedral model="   0" pdb=" CA  ASP A  88 " segid="A   "
           model="   0" pdb=" C   ASP A  88 " segid="A   "
           model="   0" pdb=" N   TYR A  89 " segid="A   "
           model="   0" pdb=" CA  TYR A  89 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.82  -15.18     0      5.00e+00 4.00e-02 9.21e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 70
       0.047 -    0.093: 56
       0.093 -    0.139: 39
       0.139 -    0.185: 10
       0.185 -    0.232: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  PRO A 117 " segid="A   "
            model="   0" pdb=" N   PRO A 117 " segid="A   "
            model="   0" pdb=" C   PRO A 117 " segid="A   "
            model="   0" pdb=" CB  PRO A 117 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.53e-01
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.36e-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 " segid="A   "   -0.068 2.00e-02 2.50e+03   3.18e-02 3.03e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.000 2.00e-02 2.50e+03   3.09e-02 2.87e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.067 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.065 2.00e-02 2.50e+03   2.84e-02 2.41e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 264
        2.28 -     2.86: 5083
        2.86 -     3.44: 5575
        3.44 -     4.02: 7450
        4.02 -     4.60: 10911
  Nonbonded interactions: 29283
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.695 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.770 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  47 " segid="A   "
            model="   0" pdb=" HZ1 LYS A 113 " segid="A   "
     model   vdw
     1.778 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.786 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.793 1.850
  ... (remaining 29278 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: (55.008, 47.03, 51.029, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: (37.982, 67.608, 54.892, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 0.74
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.81 seconds

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

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.262, 64.386, 45.175, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 0.92
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.03 seconds

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


  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.

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: 66
        1.23 -     1.42: 406
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.92e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.84e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.69e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.22e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.10e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.77 -   105.67: 78
      105.67 -   111.56: 2394
      111.56 -   117.46: 586
      117.46 -   123.36: 842
      123.36 -   129.25: 179
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.96    4.64 1.00e+00 1.00e+00 2.15e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.19    4.41 1.00e+00 1.00e+00 1.94e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.25    4.95 1.30e+00 5.92e-01 1.45e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.47    4.73 1.30e+00 5.92e-01 1.32e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 952
       15.99 -    31.99: 51
       31.99 -    47.98: 23
       47.98 -    63.98: 4
       63.98 -    79.97: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.67   23.33     0      5.00e+00 4.00e-02 2.18e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.11   15.89     0      5.00e+00 4.00e-02 1.01e+01
  dihedral model="   0" pdb=" CA  VAL A 112 " segid="A   "
           model="   0" pdb=" C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.09   14.91     0      5.00e+00 4.00e-02 8.89e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 69
       0.049 -    0.096: 61
       0.096 -    0.144: 31
       0.144 -    0.192: 14
       0.192 -    0.240: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality model="   0" pdb=" CB  ILE A  77 " segid="A   "
            model="   0" pdb=" CA  ILE A  77 " segid="A   "
            model="   0" pdb=" CG1 ILE A  77 " segid="A   "
            model="   0" pdb=" CG2 ILE A  77 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 7.74e-01
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.13e-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 " segid="A   "   -0.033 2.00e-02 2.50e+03   4.32e-02 5.60e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.110 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.025 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.090 2.00e-02 2.50e+03   4.27e-02 5.47e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.098 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.021 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03   3.43e-02 3.53e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.058 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 345
        2.30 -     2.87: 5211
        2.87 -     3.45: 5549
        3.45 -     4.02: 7400
        4.02 -     4.60: 10760
  Nonbonded interactions: 29265
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.730 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.779 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.786 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.793 1.850
  ... (remaining 29260 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}
        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: 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=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.01e+01
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.50e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.50e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.44e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.95e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.46 -   105.37: 67
      105.37 -   111.29: 2343
      111.29 -   117.20: 644
      117.20 -   123.12: 804
      123.12 -   129.03: 221
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.61    3.99 1.00e+00 1.00e+00 1.59e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.80    4.40 1.30e+00 5.92e-01 1.15e+01
  angle model="   0" pdb=" CA  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  115.91   -3.31 1.00e+00 1.00e+00 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 970
       18.00 -    35.99: 46
       35.99 -    53.99: 14
       53.99 -    71.98: 0
       71.98 -    89.98: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.04   18.96     0      5.00e+00 4.00e-02 1.44e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.10   17.90     0      5.00e+00 4.00e-02 1.28e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      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:
       0.001 -    0.049: 65
       0.049 -    0.097: 59
       0.097 -    0.146: 39
       0.146 -    0.194: 10
       0.194 -    0.243: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.074 2.00e-02 2.50e+03   3.45e-02 3.57e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.073 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.034 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.070 2.00e-02 2.50e+03   3.29e-02 3.25e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CD  ARG A 129 " segid="A   "   -0.438 9.50e-02 1.11e+02   1.46e-01 2.26e+01
        model="   0" pdb=" NE  ARG A 129 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" NH1 ARG A 129 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" NH2 ARG A 129 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb="HH11 ARG A 129 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb="HH12 ARG A 129 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb="HH21 ARG A 129 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb="HH22 ARG A 129 " segid="A   "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 313
        2.29 -     2.87: 5175
        2.87 -     3.45: 5484
        3.45 -     4.02: 7309
        4.02 -     4.60: 10704
  Nonbonded interactions: 28985
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.715 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.753 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.781 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.803 1.730
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.812 1.850
  ... (remaining 28980 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: 48
        1.23 -     1.42: 424
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.48e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.75e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.33e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.98e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.97e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.98 -   105.83: 100
      105.83 -   111.69: 2410
      111.69 -   117.54: 562
      117.54 -   123.39: 833
      123.39 -   129.24: 174
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
        model="   0" pdb=" NH2 ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     119.20  123.37   -4.17 9.00e-01 1.23e+00 2.14e+01
  angle model="   0" pdb=" NH1 ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
        model="   0" pdb=" NH2 ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     119.30  113.86    5.44 1.30e+00 5.92e-01 1.75e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.53    4.07 1.00e+00 1.00e+00 1.66e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.73    3.87 1.00e+00 1.00e+00 1.50e+01
  angle model="   0" pdb=" CA  ASP A  74 " segid="A   "
        model="   0" pdb=" CB  ASP A  74 " segid="A   "
        model="   0" pdb=" CG  ASP A  74 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  108.79    3.81 1.00e+00 1.00e+00 1.45e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 959
       15.99 -    31.98: 53
       31.98 -    47.97: 16
       47.97 -    63.96: 2
       63.96 -    79.96: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.03   26.97     0      5.00e+00 4.00e-02 2.91e+01
  dihedral model="   0" pdb=" CA  GLY A  80 " segid="A   "
           model="   0" pdb=" C   GLY A  80 " segid="A   "
           model="   0" pdb=" N   TYR A  81 " segid="A   "
           model="   0" pdb=" CA  TYR A  81 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.28   19.72     0      5.00e+00 4.00e-02 1.56e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.83   16.17     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.050: 65
       0.050 -    0.100: 68
       0.100 -    0.149: 37
       0.149 -    0.199: 4
       0.199 -    0.248: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality model="   0" pdb=" CA  PRO A 117 " segid="A   "
            model="   0" pdb=" N   PRO A 117 " segid="A   "
            model="   0" pdb=" C   PRO A 117 " segid="A   "
            model="   0" pdb=" CB  PRO A 117 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.89e-01
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    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  68 " segid="A   "    0.051 2.00e-02 2.50e+03   3.57e-02 3.82e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.090 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.051 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.070 2.00e-02 2.50e+03   3.28e-02 3.24e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.069 2.00e-02 2.50e+03   3.07e-02 2.83e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.027 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.29: 308
        2.29 -     2.87: 5118
        2.87 -     3.45: 5430
        3.45 -     4.02: 7201
        4.02 -     4.60: 10697
  Nonbonded interactions: 28754
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.793 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.806 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.816 1.850
  ... (remaining 28749 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.531, 56.775, 47.237, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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 ==============================

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: (49.47, 65.301, 48.363, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  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.

  Time building chain proxies: 0.97, per 1000 atoms: 0.44
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.402, 46.825, 50.518, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 0.61
  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.


  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   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   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: 62
        1.23 -     1.42: 410
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.17e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.13e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.45e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.39e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.35e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.33 -   106.05: 105
      106.05 -   111.76: 2435
      111.76 -   117.48: 521
      117.48 -   123.19: 817
      123.19 -   128.91: 201
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.89    4.71 1.00e+00 1.00e+00 2.21e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.53    4.07 1.00e+00 1.00e+00 1.66e+01
  angle model="   0" pdb=" CA  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.20   -3.60 1.00e+00 1.00e+00 1.29e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.65    4.55 1.30e+00 5.92e-01 1.22e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.18    3.42 1.00e+00 1.00e+00 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 938
       16.00 -    32.00: 64
       32.00 -    48.00: 23
       48.00 -    64.01: 5
       64.01 -    80.01: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.12   22.88     0      5.00e+00 4.00e-02 2.09e+01
  dihedral model="   0" pdb=" CA  GLY A  87 " segid="A   "
           model="   0" pdb=" C   GLY A  87 " segid="A   "
           model="   0" pdb=" N   ASP A  88 " segid="A   "
           model="   0" pdb=" CA  ASP A  88 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.51  -17.49     0      5.00e+00 4.00e-02 1.22e+01
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.37   16.63     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 67
       0.047 -    0.093: 54
       0.093 -    0.140: 44
       0.140 -    0.186: 8
       0.186 -    0.232: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.50e-01
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.70e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.078 2.00e-02 2.50e+03   3.65e-02 4.01e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.080 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.024 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.068 2.00e-02 2.50e+03   3.22e-02 3.11e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.021 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.045 2.00e-02 2.50e+03   2.26e-02 1.54e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.31: 371
        2.31 -     2.88: 5225
        2.88 -     3.46: 5547
        3.46 -     4.03: 7420
        4.03 -     4.60: 10756
  Nonbonded interactions: 29319
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.740 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.742 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.770 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.796 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.820 1.850
  ... (remaining 29314 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: 67
        1.23 -     1.42: 405
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.13e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.94e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.88e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.62e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.38e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.43 -   106.22: 127
      106.22 -   112.01: 2477
      112.01 -   117.80: 474
      117.80 -   123.60: 853
      123.60 -   129.39: 148
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CA  ASP A  36 " segid="A   "
        model="   0" pdb=" CB  ASP A  36 " segid="A   "
        model="   0" pdb=" CG  ASP A  36 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.74   -4.14 1.00e+00 1.00e+00 1.72e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.46    4.14 1.00e+00 1.00e+00 1.71e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.51    4.69 1.30e+00 5.92e-01 1.30e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.34: 942
       15.34 -    30.67: 59
       30.67 -    46.01: 22
       46.01 -    61.34: 8
       61.34 -    76.68: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 116 " segid="A   "
           model="   0" pdb=" C   ASP A 116 " segid="A   "
           model="   0" pdb=" N   PRO A 117 " segid="A   "
           model="   0" pdb=" CA  PRO A 117 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.76  -28.24     0      5.00e+00 4.00e-02 3.19e+01
  dihedral model="   0" pdb=" CA  ALA A 115 " segid="A   "
           model="   0" pdb=" C   ALA A 115 " segid="A   "
           model="   0" pdb=" N   ASP A 116 " segid="A   "
           model="   0" pdb=" CA  ASP A 116 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.60   20.40     0      5.00e+00 4.00e-02 1.66e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.80   17.20     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.048: 73
       0.048 -    0.094: 51
       0.094 -    0.141: 35
       0.141 -    0.188: 13
       0.188 -    0.235: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality model="   0" pdb=" CA  SER A  90 " segid="A   "
            model="   0" pdb=" N   SER A  90 " segid="A   "
            model="   0" pdb=" C   SER A  90 " segid="A   "
            model="   0" pdb=" CB  SER A  90 " segid="A   "
    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  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.87e-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 " segid="A   "   -0.145 2.00e-02 2.50e+03   6.50e-02 1.27e+02
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.134 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.055 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.080 2.00e-02 2.50e+03   3.68e-02 4.06e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.078 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.034 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.049 2.00e-02 2.50e+03   2.90e-02 2.52e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.031 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 338
        2.30 -     2.88: 5197
        2.88 -     3.45: 5542
        3.45 -     4.03: 7335
        4.03 -     4.60: 10772
  Nonbonded interactions: 29184
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.748 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.792 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.803 1.730
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HH  TYR A  68 " segid="A   "
     model   vdw
     1.819 1.730
  ... (remaining 29179 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: ""
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.757, 70.034, 48.192, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU   49": "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: ""
Symmetry information was not found, putting molecule in P1 box.

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

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

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


  Number of 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: 0.73 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: (58.84, 53.013, 57.108, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A 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

  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "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: ""
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 73
        1.23 -     1.42: 399
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.02e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.70e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.68e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.76e+00
  bond model="   0" pdb=" ND1 HIS A 135 " segid="A   "
       model="   0" pdb=" CE1 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.71e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.12 -   106.30: 141
      106.30 -   112.48: 2527
      112.48 -   118.66: 491
      118.66 -   124.84: 854
      124.84 -   131.02: 66
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.79    4.81 1.00e+00 1.00e+00 2.32e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  131.02   -6.62 1.40e+00 5.10e-01 2.24e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.80    5.40 1.30e+00 5.92e-01 1.73e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.72    3.88 1.00e+00 1.00e+00 1.51e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.24    4.96 1.30e+00 5.92e-01 1.46e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.64: 958
       16.64 -    33.28: 50
       33.28 -    49.92: 17
       49.92 -    66.56: 4
       66.56 -    83.19: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" C   TYR A  81 " segid="A   "
           model="   0" pdb=" N   TYR A  81 " segid="A   "
           model="   0" pdb=" CA  TYR A  81 " segid="A   "
           model="   0" pdb=" CB  TYR A  81 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.53    8.93     0      2.50e+00 1.60e-01 1.28e+01
  dihedral model="   0" pdb=" CA  ILE A  86 " segid="A   "
           model="   0" pdb=" C   ILE A  86 " segid="A   "
           model="   0" pdb=" N   GLY A  87 " segid="A   "
           model="   0" pdb=" CA  GLY A  87 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.41   17.59     0      5.00e+00 4.00e-02 1.24e+01
  dihedral model="   0" pdb=" CA  VAL A 112 " segid="A   "
           model="   0" pdb=" C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.65   16.35     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 82
       0.062 -    0.123: 66
       0.123 -    0.185: 25
       0.185 -    0.247: 2
       0.247 -    0.308: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  81 " segid="A   "
            model="   0" pdb=" N   TYR A  81 " segid="A   "
            model="   0" pdb=" C   TYR A  81 " segid="A   "
            model="   0" pdb=" CB  TYR A  81 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  THR A  83 " segid="A   "
            model="   0" pdb=" N   THR A  83 " segid="A   "
            model="   0" pdb=" C   THR A  83 " segid="A   "
            model="   0" pdb=" CB  THR A  83 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.86e-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 " segid="A   "    0.137 2.00e-02 2.50e+03   5.59e-02 9.37e+01
        model="   0" pdb=" CG  TYR A  81 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 " segid="A   "    0.103 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 " segid="A   "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 " segid="A   "   -0.021 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.027 2.00e-02 2.50e+03   4.26e-02 5.46e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.091 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.073 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.059 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.064 2.00e-02 2.50e+03   3.81e-02 4.36e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.048 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.33: 418
        2.33 -     2.89: 5257
        2.89 -     3.46: 5486
        3.46 -     4.03: 7230
        4.03 -     4.60: 10601
  Nonbonded interactions: 28992
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.758 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.777 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.788 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.811 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.812 1.730
  ... (remaining 28987 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: 1.12 seconds

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 46
        1.23 -     1.42: 426
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.14e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.50e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.27e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.11e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.09e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.33 -   105.32: 59
      105.32 -   111.32: 2361
      111.32 -   117.31: 642
      117.31 -   123.31: 832
      123.31 -   129.30: 185
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.82    4.78 1.00e+00 1.00e+00 2.28e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.21    5.99 1.30e+00 5.92e-01 2.12e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.25    4.35 1.00e+00 1.00e+00 1.89e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.78    5.42 1.30e+00 5.92e-01 1.74e+01
  angle model="   0" pdb=" CA  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.39   -3.79 1.00e+00 1.00e+00 1.43e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 938
       16.00 -    32.00: 68
       32.00 -    48.00: 19
       48.00 -    64.00: 4
       64.00 -    80.00: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 " segid="A   "
           model="   0" pdb=" C   HIS A 138 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.38   29.62     0      5.00e+00 4.00e-02 3.51e+01
  dihedral model="   0" pdb=" CA  HIS A 136 " segid="A   "
           model="   0" pdb=" C   HIS A 136 " segid="A   "
           model="   0" pdb=" N   HIS A 137 " segid="A   "
           model="   0" pdb=" CA  HIS A 137 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.35   26.65     0      5.00e+00 4.00e-02 2.84e+01
  dihedral model="   0" pdb=" CA  GLU A 133 " segid="A   "
           model="   0" pdb=" C   GLU A 133 " segid="A   "
           model="   0" pdb=" N   HIS A 134 " segid="A   "
           model="   0" pdb=" CA  HIS A 134 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.20   24.80     0      5.00e+00 4.00e-02 2.46e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 71
       0.047 -    0.094: 58
       0.094 -    0.141: 32
       0.141 -    0.187: 13
       0.187 -    0.234: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality model="   0" pdb=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.82e-01
  chirality model="   0" pdb=" CB  ILE A  77 " segid="A   "
            model="   0" pdb=" CA  ILE A  77 " segid="A   "
            model="   0" pdb=" CG1 ILE A  77 " segid="A   "
            model="   0" pdb=" CG2 ILE A  77 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.40e-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 " segid="A   "    0.101 2.00e-02 2.50e+03   4.84e-02 7.02e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.088 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.055 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.066 2.00e-02 2.50e+03   3.28e-02 3.23e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.065 2.00e-02 2.50e+03   2.82e-02 2.39e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 346
        2.31 -     2.88: 5159
        2.88 -     3.45: 5463
        3.45 -     4.03: 7191
        4.03 -     4.60: 10576
  Nonbonded interactions: 28735
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb="HG12 ILE A  77 " segid="A   "
            model="   0" pdb="HG21 THR A  82 " segid="A   "
     model   vdw
     1.759 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.773 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.816 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.816 1.730
  ... (remaining 28730 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.05, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.94, 46.779, 52.138, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 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.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

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

  Time building geometry restraints manager: 1.21 seconds

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  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.

  Time building chain proxies: 1.07, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.138, 61.944, 61.142, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 57
        1.23 -     1.42: 415
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   1" pdb=" CZ  ARG A 127 " segid="A   "
       model="   1" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.57e+00
  bond model="   1" pdb=" CZ  ARG A  21 " segid="A   "
       model="   1" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.10e+00
  bond model="   1" pdb=" CD2 HIS A 139 " segid="A   "
       model="   1" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.74e+00
  bond model="   1" pdb=" CD2 HIS A 136 " segid="A   "
       model="   1" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.06e+00
  bond model="   1" pdb=" CZ  ARG A  58 " segid="A   "
       model="   1" pdb=" NH2 ARG A  58 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.98e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.58 -   105.57: 74
      105.57 -   111.56: 2407
      111.56 -   117.56: 583
      117.56 -   123.55: 870
      123.55 -   129.54: 145
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   1" pdb=" OE1 GLN A  28 " segid="A   "
        model="   1" pdb=" CD  GLN A  28 " segid="A   "
        model="   1" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.80    4.80 1.00e+00 1.00e+00 2.31e+01
  angle model="   1" pdb=" CB  HIS A 134 " segid="A   "
        model="   1" pdb=" CG  HIS A 134 " segid="A   "
        model="   1" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.91    5.29 1.30e+00 5.92e-01 1.66e+01
  angle model="   1" pdb=" OE1 GLN A 100 " segid="A   "
        model="   1" pdb=" CD  GLN A 100 " segid="A   "
        model="   1" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.62    3.98 1.00e+00 1.00e+00 1.58e+01
  angle model="   1" pdb=" CB  HIS A 135 " segid="A   "
        model="   1" pdb=" CG  HIS A 135 " segid="A   "
        model="   1" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.18    5.02 1.30e+00 5.92e-01 1.49e+01
  angle model="   1" pdb=" CD  ARG A  21 " segid="A   "
        model="   1" pdb=" NE  ARG A  21 " segid="A   "
        model="   1" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.54   -5.14 1.40e+00 5.10e-01 1.35e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 961
       17.70 -    35.41: 47
       35.41 -    53.11: 18
       53.11 -    70.81: 3
       70.81 -    88.51: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   1" pdb=" CA  TYR A  81 " segid="A   "
           model="   1" pdb=" C   TYR A  81 " segid="A   "
           model="   1" pdb=" N   THR A  82 " segid="A   "
           model="   1" pdb=" CA  THR A  82 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.86   31.14     0      5.00e+00 4.00e-02 3.88e+01
  dihedral model="   1" pdb=" CA  HIS A 137 " segid="A   "
           model="   1" pdb=" C   HIS A 137 " segid="A   "
           model="   1" pdb=" N   HIS A 138 " segid="A   "
           model="   1" pdb=" CA  HIS A 138 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.82   26.18     0      5.00e+00 4.00e-02 2.74e+01
  dihedral model="   1" pdb=" CA  HIS A 135 " segid="A   "
           model="   1" pdb=" C   HIS A 135 " segid="A   "
           model="   1" pdb=" N   HIS A 136 " segid="A   "
           model="   1" pdb=" CA  HIS A 136 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.50   22.50     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.048: 70
       0.048 -    0.094: 56
       0.094 -    0.140: 32
       0.140 -    0.186: 13
       0.186 -    0.232: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   1" pdb=" CA  PHE A  45 " segid="A   "
            model="   1" pdb=" N   PHE A  45 " segid="A   "
            model="   1" pdb=" C   PHE A  45 " segid="A   "
            model="   1" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality model="   1" pdb=" CA  LYS A  85 " segid="A   "
            model="   1" pdb=" N   LYS A  85 " segid="A   "
            model="   1" pdb=" C   LYS A  85 " segid="A   "
            model="   1" pdb=" CB  LYS A  85 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality model="   1" pdb=" CA  PRO A 117 " segid="A   "
            model="   1" pdb=" N   PRO A 117 " segid="A   "
            model="   1" pdb=" C   PRO A 117 " segid="A   "
            model="   1" pdb=" CB  PRO A 117 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  PHE A  67 " segid="A   "   -0.095 2.00e-02 2.50e+03   3.70e-02 4.10e+01
        model="   1" pdb=" CG  PHE A  67 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 PHE A  67 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 PHE A  67 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 PHE A  67 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 PHE A  67 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  PHE A  67 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 PHE A  67 " segid="A   "    0.039 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 PHE A  67 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 PHE A  67 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 PHE A  67 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   1" pdb=" HZ  PHE A  67 " segid="A   "   -0.049 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  12 " segid="A   "   -0.077 2.00e-02 2.50e+03   3.54e-02 3.76e+01
        model="   1" pdb=" CG  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  12 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  12 " segid="A   "   -0.075 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  12 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  12 " segid="A   "    0.033 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   1" pdb=" CB  TYR A  81 " segid="A   "    0.087 2.00e-02 2.50e+03   3.51e-02 3.70e+01
        model="   1" pdb=" CG  TYR A  81 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   1" pdb=" CD1 TYR A  81 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   1" pdb=" CD2 TYR A  81 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   1" pdb=" CE1 TYR A  81 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   1" pdb=" CE2 TYR A  81 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   1" pdb=" CZ  TYR A  81 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   1" pdb=" OH  TYR A  81 " segid="A   "    0.059 2.00e-02 2.50e+03
        model="   1" pdb=" HD1 TYR A  81 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   1" pdb=" HD2 TYR A  81 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   1" pdb=" HE1 TYR A  81 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   1" pdb=" HE2 TYR A  81 " segid="A   "   -0.010 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.28: 289
        2.28 -     2.86: 5098
        2.86 -     3.44: 5575
        3.44 -     4.02: 7089
        4.02 -     4.60: 10624
  Nonbonded interactions: 28675
  Sorted by model distance:
  nonbonded model="   1" pdb=" OE1 GLU A  75 " segid="A   "
            model="   1" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.705 1.850
  nonbonded model="   1" pdb=" OD1 ASP A  74 " segid="A   "
            model="   1" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.720 1.850
  nonbonded model="   1" pdb=" OD1 ASP A  44 " segid="A   "
            model="   1" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.779 1.850
  nonbonded model="   1" pdb=" OE2 GLU A  16 " segid="A   "
            model="   1" pdb=" HZ3 LYS A  19 " segid="A   "
     model   vdw
     1.815 1.730
  nonbonded model="   1" pdb=" O   LEU A  61 " segid="A   "
            model="   1" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.816 1.850
  ... (remaining 28670 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: 82
        1.23 -     1.43: 390
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.96e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.92e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.26e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.93e+00
  bond model="   0" pdb=" ND1 HIS A 136 " segid="A   "
       model="   0" pdb=" CE1 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.68e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.49 -   106.25: 132
      106.25 -   112.00: 2453
      112.00 -   117.76: 496
      117.76 -   123.51: 840
      123.51 -   129.27: 158
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.20    4.40 1.00e+00 1.00e+00 1.94e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      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 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      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  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.01    3.59 1.00e+00 1.00e+00 1.29e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 954
       15.94 -    31.87: 54
       31.87 -    47.81: 16
       47.81 -    63.75: 7
       63.75 -    79.68: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.02   30.98     0      5.00e+00 4.00e-02 3.84e+01
  dihedral model="   0" pdb=" CA  GLY A  87 " segid="A   "
           model="   0" pdb=" C   GLY A  87 " segid="A   "
           model="   0" pdb=" N   ASP A  88 " segid="A   "
           model="   0" pdb=" CA  ASP A  88 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.35  -17.65     0      5.00e+00 4.00e-02 1.25e+01
  dihedral model="   0" pdb=" CA  VAL A 112 " segid="A   "
           model="   0" pdb="   Time building chain proxies: 0.98, per 1000 atoms: 0.44
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.122, 43.314, 58.342, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.58   17.42     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 72
       0.046 -    0.091: 47
       0.091 -    0.137: 39
       0.137 -    0.183: 16
       0.183 -    0.228: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    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  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.23e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 7.70e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.072 2.00e-02 2.50e+03   3.33e-02 3.32e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.044 2.00e-02 2.50e+03   3.28e-02 3.24e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.084 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.046 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03   3.16e-02 3.00e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 286
        2.28 -     2.86: 5105
        2.86 -     3.44: 5606
        3.44 -     4.02: 7404
        4.02 -     4.60: 11033
  Nonbonded interactions: 29434
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.700 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.712 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.808 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.814 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.836 1.730
  ... (remaining 29429 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 92
        1.23 -     1.43: 380
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.37e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.29e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.49e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.07e+00
  bond model="   0" pdb=" ND1 HIS A 134 " segid="A   "
       model="   0" pdb=" CE1 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.05e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.57 -   104.74: 37
      104.74 -   110.91: 2307
      110.91 -   117.09: 705
      117.09 -   123.26: 836
      123.26 -   129.43: 194
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A  52 " segid="A   "
        model="   0" pdb=" N   LEU A  53 " segid="A   "
        model="   0" pdb=" CA  LEU A  53 " segid="A   "
      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 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.51    4.09 1.00e+00 1.00e+00 1.67e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      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  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      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 -    17.87: 971
       17.87 -    35.73: 33
       35.73 -    53.60: 15
       53.60 -    71.46: 9
       71.46 -    89.33: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  49 " segid="A   "
           model="   0" pdb=" CG  GLU A  49 " segid="A   "
           model="   0" pdb=" CD  GLU A  49 " segid="A   "
           model="   0" pdb=" OE1 GLU A  49 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.33   89.33     1      3.00e+01 1.11e-03 1.05e+01
  dihedral model="   0" pdb=" CB  GLU A  84 " segid="A   "
           model="   0" pdb=" CG  GLU A  84 " segid="A   "
           model="   0" pdb=" CD  GLU A  84 " segid="A   "
           model="   0" pdb=" OE1 GLU A  84 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.57  -88.57     1      3.00e+01 1.11e-03 1.04e+01
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.44   86.44     1      3.00e+01 1.11e-03 1.00e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 77
       0.046 -    0.091: 45
       0.091 -    0.137: 39
       0.137 -    0.182: 13
       0.182 -    0.227: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    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 123 " segid="A   "
            model="   0" pdb=" N   GLU A 123 " segid="A   "
            model="   0" pdb=" C   GLU A 123 " segid="A   "
            model="   0" pdb=" CB  GLU A 123 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.43e-01
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.11e-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 " segid="A   "   -0.071 2.00e-02 2.50e+03   5.59e-02 9.39e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.139 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.086 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.035 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.096 2.00e-02 2.50e+03   3.94e-02 4.67e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.074 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.078 2.00e-02 2.50e+03   3.67e-02 4.04e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.079 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.036 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 427
        2.32 -     2.89: 5348
        2.89 -     3.46: 5833
        3.46 -     4.03: 7791
        4.03 -     4.60: 11360
  Nonbonded interactions: 30759
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.749 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.785 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.814 1.730
  nonbonded model="   0" pdb=" OE1 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.831 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A  10 " segid="A   "
            model="   0" pdb=" OD2 ASP A  23 " segid="A   "
     model   vdw
     1.832 1.730
  ... (remaining 30754 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}
  Time building chain proxies: 0.88, per 1000 atoms: 0.40
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.214, 47.758, 59.608, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.25 seconds

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  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 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: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 55
        1.23 -     1.42: 417
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.61e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.17e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.88e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.63e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.38e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.98 -   106.00: 96
      106.00 -   112.01: 2518
      112.01 -   118.03: 494
      118.03 -   124.04: 864
      124.04 -   130.06: 107
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.90    4.70 1.00e+00 1.00e+00 2.20e+01
  angle model="   0" pdb=" N   ALA A 124 " segid="A   "
        model="   0" pdb=" CA  ALA A 124 " segid="A   "
        model="   0" pdb=" CB  ALA A 124 " segid="A   "
      ideal   model   delta    sigma   weight residual
     110.40  103.62    6.78 1.50e+00 4.44e-01 2.04e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.30    4.30 1.00e+00 1.00e+00 1.85e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.06   -5.66 1.40e+00 5.10e-01 1.63e+01
  angle model="   0" pdb=" CA  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      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 -    15.55: 953
       15.55 -    31.11: 57
       31.11 -    46.66: 17
       46.66 -    62.22: 3
       62.22 -    77.77: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.09   15.91     0      5.00e+00 4.00e-02 1.01e+01
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.34    7.74     0      2.50e+00 1.60e-01 9.59e+00
  dihedral model="   0" pdb=" CA  ALA A  48 " segid="A   "
           model="   0" pdb=" C   ALA A  48 " segid="A   "
           model="   0" pdb=" N   GLU A  49 " segid="A   "
           model="   0" pdb=" CA  GLU A  49 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.37   14.63     0      5.00e+00 4.00e-02 8.56e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 71
       0.052 -    0.104: 64
       0.104 -    0.155: 31
       0.155 -    0.207: 7
       0.207 -    0.258: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.11e+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 " segid="A   "    0.046 2.00e-02 2.50e+03   5.88e-02 1.04e+02
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.149 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.097 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.058 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.133 2.00e-02 2.50e+03   5.40e-02 8.75e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.097 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.018 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03   3.35e-02 3.37e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.056 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 339
        2.30 -     2.87: 5217
        2.87 -     3.45: 5562
        3.45 -     4.02: 7452
        4.02 -     4.60: 10955
  Nonbonded interactions: 29525
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.744 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.780 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.805 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.805 1.730
  ... (remaining 29520 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: 0.85
  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.

  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=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.14e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.73e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.12e+00
  bond model="   0" pdb=" ND1 HIS A 135 " segid="A   "
       model="   0" pdb=" CE1 HIS A 135 " segid="A   "
    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  58 " segid="A   "
       model="   0" pdb=" NH2 ARG A  58 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.01e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.66 -   105.58: 73
      105.58 -   111.49: 2390
      111.49 -   117.41: 604
      117.41 -   123.32: 825
      123.32 -   129.24: 187
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.76    4.84 1.00e+00 1.00e+00 2.34e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.54    5.66 1.30e+00 5.92e-01 1.89e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.33    4.87 1.30e+00 5.92e-01 1.40e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.56    4.64 1.30e+00 5.92e-01 1.27e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.61: 944
       15.61 -    31.22: 67
       31.22 -    46.82: 16
       46.82 -    62.43: 4
       62.43 -    78.04: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LEU A 132 " segid="A   "
           model="   0" pdb=" C   LEU A 132 " segid="A   "
           model="   0" pdb=" N   GLU A 133 " segid="A   "
           model="   0" pdb=" CA  GLU A 133 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.95   41.05     0      5.00e+00 4.00e-02 6.74e+01
  dihedral model="   0" pdb=" CA  HIS A 138 " segid="A   "
           model="   0" pdb=" C   HIS A 138 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.37   29.63     0      5.00e+00 4.00e-02 3.51e+01
  dihedral model="   0" pdb=" CA  HIS A 134 " segid="A   "
           model="   0" pdb=" C   HIS A 134 " segid="A   "
           model="   0" pdb=" N   HIS A 135 " segid="A   "
           model="   0" pdb=" CA  HIS A 135 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.71   24.29     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 71
       0.046 -    0.091: 54
       0.091 -    0.135: 32
       0.135 -    0.180: 18
       0.180 -    0.225: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  SER A  46 " segid="A   "
            model="   0" pdb=" N   SER A  46 " segid="A   "
            model="   0" pdb=" C   SER A  46 " segid="A   "
            model="   0" pdb=" CB  SER A  46 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.62e-01
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.43e-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 " segid="A   "   -0.177 2.00e-02 2.50e+03   9.25e-02 2.56e+02
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.220 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.067 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.093 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.051 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.068 2.00e-02 2.50e+03   3.29e-02 3.25e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.023 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.073 2.00e-02 2.50e+03   2.82e-02 2.39e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 333
        2.30 -     2.88: 5175
        2.88 -     3.45: 5526
        3.45 -     4.03: 7182
        4.03 -     4.60: 10663
  Nonbonded interactions: 28879
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.810 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.811 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.815 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.817 1.730
  ... (remaining 28874 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.285, 43.335, 48.433, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 76
        1.23 -     1.43: 396
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.30e+00
  bond model="   0" pdb=" ND1 HIS A 137 " segid="A   "
       model="   0" pdb=" CE1 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.40e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.18e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.99e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.71e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.32 -   105.23: 55
      105.23 -   111.14: 2337
      111.14 -   117.06: 645
      117.06 -   122.97: 814
      122.97 -   128.88: 228
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.51    4.09 1.00e+00 1.00e+00 1.67e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.25    4.95 1.30e+00 5.92e-01 1.45e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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 118 " segid="A   "
        model="   0" pdb=" CB  ASP A 118 " segid="A   "
        model="   0" pdb=" CG  ASP A 118 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.14   -3.54 1.00e+00 1.00e+00 1.25e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 974
       15.94 -    31.87: 39
       31.87 -    47.81: 14
       47.81 -    63.74: 4
       63.74 -    79.68: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 136 " segid="A   "
           model="   0" pdb=" C   HIS A 136 " segid="A   "
           model="   0" pdb=" N   HIS A 137 " segid="A   "
           model="   0" pdb=" CA  HIS A 137 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.93   19.07     0      5.00e+00 4.00e-02 1.45e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.99   17.01     0      5.00e+00 4.00e-02 1.16e+01
  dihedral model="   0" pdb=" CA  HIS A 138 " segid="A   "
           model="   0" pdb=" C   HIS A 138 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.65   16.35     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 76
       0.047 -    0.095: 53
       0.095 -    0.142: 37
       0.142 -    0.189: 9
       0.189 -    0.236: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality model="   0" pdb=" CG  LEU A  99 " segid="A   "
            model="   0" pdb=" CB  LEU A  99 " segid="A   "
            model="   0" pdb=" CD1 LEU A  99 " segid="A   "
            model="   0" pdb=" CD2 LEU A  99 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.19 2.00e-01 2.50e+01 8.69e-01
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A 118 " segid="A   "   -0.029 2.00e-02 2.50e+03   5.74e-02 3.30e+01
        model="   0" pdb=" CG  ASP A 118 " segid="A   "    0.099 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A 118 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A 118 " segid="A   "   -0.035 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.071 2.00e-02 2.50e+03   3.17e-02 3.01e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.028 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.066 2.00e-02 2.50e+03   2.97e-02 2.65e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.29: 296
        2.29 -     2.87: 5190
        2.87 -     3.45: 5542
        3.45 -     4.02: 7381
        4.02 -     4.60: 10873
  Nonbonded interactions: 29282
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.718 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.797 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.805 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.808 1.730
  nonbonded model="   0" pdb=" OD2 ASP A 118 " segid="A   "
            model="   0" pdb=" HZ1 LYS A 125 " segid="A   "
     model   vdw
     1.823 1.730
  ... (remaining 29277 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.07, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.001, 73.386, 41.686, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.09
  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.


  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: ""
  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=" CB  THR A  82 " segid="A   "
       model="   0" pdb=" OG1 THR A  82 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.433  1.388  0.045 1.60e-02 3.91e+03 8.01e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.18e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.53e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.42e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.10e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.57 -   106.34: 131
      106.34 -   112.11: 2493
      112.11 -   117.88: 464
      117.88 -   123.66: 853
      123.66 -   129.43: 138
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.84    4.76 1.00e+00 1.00e+00 2.27e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.19    4.41 1.00e+00 1.00e+00 1.95e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.43   -5.03 1.40e+00 5.10e-01 1.29e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.62    4.58 1.30e+00 5.92e-01 1.24e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 947
       16.01 -    32.03: 54
       32.03 -    48.04: 19
       48.04 -    64.06: 10
       64.06 -    80.07: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      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  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.54   15.46     0      5.00e+00 4.00e-02 9.57e+00
  dihedral model="   0" pdb=" N   HIS A 134 " segid="A   "
           model="   0" pdb=" CA  HIS A 134 " segid="A   "
           model="   0" pdb=" CB  HIS A 134 " segid="A   "
           model="   0" pdb=" CG  HIS A 134 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.99  -58.01     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 76
       0.047 -    0.094: 52
       0.094 -    0.141: 30
       0.141 -    0.188: 17
       0.188 -    0.234: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.43e-01
  chirality model="   0" pdb=" CA  ILE A  86 " segid="A   "
            model="   0" pdb=" N   ILE A  86 " segid="A   "
            model="   0" pdb=" C   ILE A  86 " segid="A   "
            model="   0" pdb=" CB  ILE A  86 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.51e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.091 2.00e-02 2.50e+03   3.93e-02 4.64e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.081 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.019 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.055 2.00e-02 2.50e+03   3.44e-02 3.54e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.050 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 " segid="A   "    0.060 2.00e-02 2.50e+03   3.55e-02 2.51e+01
        model="   0" pdb=" CG  HIS A 139 " segid="A   "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 " segid="A   "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 " segid="A   "    0.031 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 328
        2.30 -     2.87: 5138
        2.87 -     3.45: 5553
        3.45 -     4.02: 7314
        4.02 -     4.60: 10662
  Nonbonded interactions: 28995
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.722 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.750 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.773 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.806 1.730
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.810 1.850
  ... (remaining 28990 not shown)

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

  Number of 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: 1.12 seconds

  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: (48.833, 47.901, 68.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 0.79
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.89 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: 98
        1.23 -     1.43: 374
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.21e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.51e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.29e+00
  bond model="   0" pdb=" ND1 HIS A 136 " segid="A   "
       model="   0" pdb=" CE1 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.14e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.06e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.43 -   106.47: 145
      106.47 -   112.51: 2534
      112.51 -   118.55: 474
      118.55 -   124.59: 838
      124.59 -   130.63: 88
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.13    6.07 1.30e+00 5.92e-01 2.18e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.07    4.53 1.00e+00 1.00e+00 2.05e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.63   -6.23 1.40e+00 5.10e-01 1.98e+01
  angle model="   0" pdb=" CA  ASP A 118 " segid="A   "
        model="   0" pdb=" CB  ASP A 118 " segid="A   "
        model="   0" pdb=" CG  ASP A 118 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.86   -4.26 1.00e+00 1.00e+00 1.82e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.55    4.05 1.00e+00 1.00e+00 1.64e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 968
       17.99 -    35.98: 42
       35.98 -    53.97: 16
       53.97 -    71.96: 3
       71.96 -    89.95: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 " segid="A   "
           model="   0" pdb=" C   HIS A 138 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.52   18.48     0      5.00e+00 4.00e-02 1.37e+01
  dihedral model="   0" pdb=" CG  ARG A 129 " segid="A   "
           model="   0" pdb=" CD  ARG A 129 " segid="A   "
           model="   0" pdb=" NE  ARG A 129 " segid="A   "
           model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.91   44.91     2      1.50e+01 4.44e-03 1.06e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.70   16.30     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.050: 71
       0.050 -    0.099: 58
       0.099 -    0.148: 37
       0.148 -    0.197: 8
       0.197 -    0.246: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality model="   0" pdb=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    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  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.06e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.041 2.00e-02 2.50e+03   6.11e-02 1.12e+02
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.118 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.069 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.116 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.089 2.00e-02 2.50e+03   4.00e-02 4.80e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.083 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.033 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "    0.082 2.00e-02 2.50e+03   3.78e-02 4.28e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.039 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.32: 387
        2.32 -     2.89: 5280
        2.89 -     3.46: 5518
        3.46 -     4.03: 7506
        4.03 -     4.60: 10899
  Nonbonded interactions: 29590
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.744 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.774 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.780 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.801 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.810 1.850
  ... (remaining 29585 not shown)

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

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

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (40.823, 51.642, 49.952, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 47
        1.23 -     1.42: 425
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.408 -0.034 1.10e-02 8.26e+03 9.59e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.65e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.57e+00
  bond model="   0" pdb=" ND1 HIS A 135 " segid="A   "
       model="   0" pdb=" CE1 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.44e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.79 -   105.92: 92
      105.92 -   112.05: 2536
      112.05 -   118.18: 496
      118.18 -   124.31: 868
      124.31 -   130.44: 87
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.64    3.96 1.00e+00 1.00e+00 1.57e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.06    5.14 1.30e+00 5.92e-01 1.56e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CA  HIS A 136 " segid="A   "
        model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     113.80  117.55   -3.75 1.00e+00 1.00e+00 1.40e+01
  angle model="   0" pdb=" CD2 HIS A 136 " segid="A   "
        model="   0" pdb=" NE2 HIS A 136 " segid="A   "
        model="   0" pdb=" CE1 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     109.00  105.38    3.62 1.00e+00 1.00e+00 1.31e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.74: 986
       18.74 -    37.48: 32
       37.48 -    56.22: 10
       56.22 -    74.96: 2
       74.96 -    93.70: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  49 " segid="A   "
           model="   0" pdb=" CG  GLU A  49 " segid="A   "
           model="   0" pdb=" CD  GLU A  49 " segid="A   "
           model="   0" pdb=" OE1 GLU A  49 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -93.70   93.70     1      3.00e+01 1.11e-03 1.14e+01
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.88  -83.88     1      3.00e+01 1.11e-03 9.53e+00
  dihedral model="   0" pdb=" CB  GLU A  32 " segid="A   "
           model="   0" pdb=" CG  GLU A  32 " segid="A   "
           model="   0" pdb=" CD  GLU A  32 " segid="A   "
           model="   0" pdb=" OE1 GLU A  32 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.45   79.45     1      3.00e+01 1.11e-03 8.71e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.048: 87
       0.048 -    0.094: 49
       0.094 -    0.141: 31
       0.141 -    0.187: 7
       0.187 -    0.234: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ARG A 127 " segid="A   "
            model="   0" pdb=" N   ARG A 127 " segid="A   "
            model="   0" pdb=" C   ARG A 127 " segid="A   "
            model="   0" pdb=" CB  ARG A 127 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.90e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A  43 " segid="A   "   -0.063 2.00e-02 2.50e+03   4.18e-02 3.49e+01
        model="   0" pdb=" CG  HIS A  43 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 " segid="A   "    0.075 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 " segid="A   "   -0.053 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "   -0.031 2.00e-02 2.50e+03   3.36e-02 3.39e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.081 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.006 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 " segid="A   "   -0.075 2.00e-02 2.50e+03   3.07e-02 2.84e+01
        model="   0" pdb=" CG  TYR A  81 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 " segid="A   "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 " segid="A   "    0.010 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 286
        2.30 -     2.87: 5191
        2.87 -     3.45: 5470
        3.45 -     4.02: 7305
        4.02 -     4.60: 10788
  Nonbonded interactions: 29040
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A 120 " segid="A   "
            model="   0" pdb=" HZ1 LYS A 125 " segid="A   "
     model   vdw
     1.719 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.754 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.798 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.804 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.829 1.730
  ... (remaining 29035 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: 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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.30e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.53e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.41e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.30e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.26e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.14 -   105.94: 101
      105.94 -   111.73: 2421
      111.73 -   117.53: 556
      117.53 -   123.33: 818
      123.33 -   129.13: 183
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.11    4.49 1.00e+00 1.00e+00 2.02e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.33    4.27 1.00e+00 1.00e+00 1.82e+01
  angle model="   0" pdb=" CA  ASP A 118 " segid="A   "
        model="   0" pdb=" C   ASP A 118 " segid="A   "
        model="   0" pdb=" N   LEU A 119 " segid="A   "
      ideal   model   delta    sigma   weight residual
     116.20  123.38   -7.18 2.00e+00 2.50e-01 1.29e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.13   -4.73 1.40e+00 5.10e-01 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 950
       16.01 -    32.01: 63
       32.01 -    48.02: 14
       48.02 -    64.03: 3
       64.03 -    80.03: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.92   19.08     0      5.00e+00 4.00e-02 1.46e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.94   16.06     0      5.00e+00 4.00e-02 1.03e+01
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.59    7.99     0      2.50e+00 1.60e-01 1.02e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.051: 77
       0.051 -    0.102: 59
       0.102 -    0.153: 33
       0.153 -    0.203: 6
       0.203 -    0.254: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    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  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.16e-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 " segid="A   "    0.086 2.00e-02 2.50e+03   3.89e-02 4.53e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.082 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.035 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.056 2.00e-02 2.50e+03   3.54e-02 3.75e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.092 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.035 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.047 2.00e-02 2.50e+03   3.47e-02 3.61e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.052 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 275
        2.28 -     2.86: 5102
        2.86 -     3.44: 5573
        3.44 -     4.02: 7445
        4.02 -     4.60: 10882
  Nonbonded interactions: 29277
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.697 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.794 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.800 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.807 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.809 1.730
  ... (remaining 29272 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: 1.11 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: {'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: 0.59
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 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=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.409 -0.035 1.10e-02 8.26e+03 9.94e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.73e+00
  bond model="   0" pdb=" CE1 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.52e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.40e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.18e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.46 -   106.20: 108
      106.20 -   111.94: 2491
      111.94 -   117.69: 497
      117.69 -   123.43: 816
      123.43 -   129.17: 167
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 139 " segid="A   "
        model="   0" pdb=" CG  HIS A 139 " segid="A   "
        model="   0" pdb=" CD2 HIS A 139 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.25    5.95 1.30e+00 5.92e-01 2.09e+01
  angle model="   0" pdb=" CG  LYS A 125 " segid="A   "
        model="   0" pdb=" CD  LYS A 125 " segid="A   "
        model="   0" pdb=" CE  LYS A 125 " segid="A   "
      ideal   model   delta    sigma   weight residual
     111.30  101.64    9.66 2.30e+00 1.89e-01 1.77e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.46    4.14 1.00e+00 1.00e+00 1.71e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.51    4.09 1.00e+00 1.00e+00 1.67e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.39: 984
       16.39 -    32.78: 25
       32.78 -    49.17: 15
       49.17 -    65.57: 5
       65.57 -    81.96: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.96  -81.96     1      3.00e+01 1.11e-03 9.17e+00
  dihedral model="   0" pdb=" CB  GLU A  49 " segid="A   "
           model="   0" pdb=" CG  GLU A  49 " segid="A   "
           model="   0" pdb=" CD  GLU A  49 " segid="A   "
           model="   0" pdb=" OE1 GLU A  49 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -81.25   81.25     1      3.00e+01 1.11e-03 9.04e+00
  dihedral model="   0" pdb=" CB  GLU A  32 " segid="A   "
           model="   0" pdb=" CG  GLU A  32 " segid="A   "
           model="   0" pdb=" CD  GLU A  32 " segid="A   "
           model="   0" pdb=" OE1 GLU A  32 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   78.52  -78.52     1      3.00e+01 1.11e-03 8.54e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 81
       0.045 -    0.090: 53
       0.090 -    0.135: 28
       0.135 -    0.181: 13
       0.181 -    0.226: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.32e-01
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.56e-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 " segid="A   "   -0.142 2.00e-02 2.50e+03   7.30e-02 1.60e+02
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.165 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.075 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.078 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.087 2.00e-02 2.50e+03   4.23e-02 5.38e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.092 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.013 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 " segid="A   "    0.062 2.00e-02 2.50e+03   2.72e-02 2.22e+01
        model="   0" pdb=" CG  TYR A  81 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 " segid="A   "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 " segid="A   "   -0.026 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.34: 467
        2.34 -     2.90: 5217
        2.90 -     3.47: 5390
        3.47 -     4.03: 7332
        4.03 -     4.60: 10399
  Nonbonded interactions: 28805
  Sorted by model distance:
  nonbonded model="   0" pdb=" HH  TYR A  81 " segid="A   "
            model="   0" pdb=" HD2 TYR A  91 " segid="A   "
     model   vdw
     1.773 2.100
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.794 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.807 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.818 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ1 LYS A 101 " segid="A   "
     model   vdw
     1.827 1.730
  ... (remaining 28800 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: 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=" CB  THR A  82 " segid="A   "
       model="   0" pdb=" OG1 THR A  82 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.433  1.390  0.043 1.60e-02 3.91e+03 7.27e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.08e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.77e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    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=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.90e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.98 -   106.61: 170
      106.61 -   112.24: 2464
      112.24 -   117.87: 449
      117.87 -   123.49: 845
      123.49 -   129.12: 151
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.63    3.97 1.00e+00 1.00e+00 1.58e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.70    3.90 1.00e+00 1.00e+00 1.52e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.75    4.45 1.30e+00 5.92e-01 1.17e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.12   -4.72 1.40e+00 5.10e-01 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.58: 956
       15.58 -    31.15: 49
       31.15 -    46.73: 21
       46.73 -    62.31: 4
       62.31 -    77.88: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 " segid="A   "
           model="   0" pdb=" C   HIS A 138 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.07   21.93     0      5.00e+00 4.00e-02 1.92e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.99   21.01     0      5.00e+00 4.00e-02 1.77e+01
  dihedral model="   0" pdb=" C   HIS A 137 " segid="A   "
           model="   0" pdb=" N   HIS A 137 " segid="A   "
           model="   0" pdb=" CA  HIS A 137 " segid="A   "
           model="   0" pdb=" CB  HIS A 137 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.86    8.26     0      2.50e+00 1.60e-01 1.09e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 86
       0.059 -    0.117: 58
       0.117 -    0.175: 28
       0.175 -    0.234: 3
       0.234 -    0.292: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 137 " segid="A   "
            model="   0" pdb=" N   HIS A 137 " segid="A   "
            model="   0" pdb=" C   HIS A 137 " segid="A   "
            model="   0" pdb=" CB  HIS A 137 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.93e-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 " segid="A   "   -0.092 2.00e-02 2.50e+03   5.22e-02 8.17e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.101 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.076 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.077 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.079 2.00e-02 2.50e+03   3.50e-02 3.67e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.058 2.00e-02 2.50e+03   3.33e-02 3.32e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.083 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.037 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.29: 312
        2.29 -     2.87: 5134
        2.87 -     3.45: 5493
        3.45 -     4.02: 7191
        4.02 -     4.60: 10560
  Nonbonded interactions: 28690
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.718 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.782 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.800 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.804 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.822 1.850
  ... (remaining 28685 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: (79.577, 55.68, 36.754, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.17 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.92e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.28e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.20e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.06e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.59e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.75 -   105.68: 86
      105.68 -   111.62: 2420
      111.62 -   117.55: 568
      117.55 -   123.48: 848
      123.48 -   129.41: 157
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.92    4.68 1.00e+00 1.00e+00 2.19e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.29    4.31 1.00e+00 1.00e+00 1.86e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.41   -5.01 1.40e+00 5.10e-01 1.28e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.21: 944
       15.21 -    30.43: 62
       30.43 -    45.64: 21
       45.64 -    60.86: 4
       60.86 -    76.07: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.32   32.68     0      5.00e+00 4.00e-02 4.27e+01
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.48   31.52     0      5.00e+00 4.00e-02 3.97e+01
  dihedral model="   0" pdb=" CA  GLU A 133 " segid="A   "
           model="   0" pdb=" C   GLU A 133 " segid="A   "
           model="   0" pdb=" N   HIS A 134 " segid="A   "
           model="   0" pdb=" CA  HIS A 134 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.85   16.15     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 83
       0.052 -    0.104: 60
       0.104 -    0.156: 24
       0.156 -    0.208: 8
       0.208 -    0.260: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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=" CA  TYR A  81 " segid="A   "
            model="   0" pdb=" N   TYR A  81 " segid="A   "
            model="   0" pdb=" C   TYR A  81 " segid="A   "
            model="   0" pdb=" CB  TYR A  81 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality model="   0" pdb=" CB  VAL A 126 " segid="A   "
            model="   0" pdb=" CA  VAL A 126 " segid="A   "
            model="   0" pdb=" CG1 VAL A 126 " segid="A   "
            model="   0" pdb=" CG2 VAL A 126 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.82    0.19 2.00e-01 2.50e+01 9.46e-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 " segid="A   "   -0.068 2.00e-02 2.50e+03   3.42e-02 3.51e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.021 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.036 2.00e-02 2.50e+03   2.97e-02 2.65e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.076 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.018 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.063 2.00e-02 2.50e+03   2.88e-02 2.49e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.027 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 329
        2.30 -     2.87: 5236
        2.87 -     3.45: 5606
        3.45 -     4.02: 7506
        4.02 -     4.60: 10995
  Nonbonded interactions: 29672
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.722 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.792 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.811 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.817 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.817 1.730
  ... (remaining 29667 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.

  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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.14e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.99e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.64e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.40e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.18e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.75 -   105.61: 80
      105.61 -   111.47: 2362
      111.47 -   117.32: 612
      117.32 -   123.18: 822
      123.18 -   129.04: 203
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.19    4.41 1.00e+00 1.00e+00 1.95e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.24    4.36 1.00e+00 1.00e+00 1.90e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      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 -    16.65: 959
       16.65 -    33.30: 47
       33.30 -    49.94: 20
       49.94 -    66.59: 4
       66.59 -    83.24: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.15   26.85     0      5.00e+00 4.00e-02 2.88e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.76   16.24     0      5.00e+00 4.00e-02 1.06e+01
  dihedral model="   0" pdb=" CA  VAL A 112 " segid="A   "
           model="   0" pdb=" C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.85   16.15     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 76
       0.049 -    0.098: 57
       0.098 -    0.147: 33
       0.147 -    0.196: 9
       0.196 -    0.245: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.25 2.00e-01 2.50e+01 1.50e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    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  91 " segid="A   "    0.101 2.00e-02 2.50e+03   4.34e-02 5.66e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.081 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.028 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.082 2.00e-02 2.50e+03   3.71e-02 4.13e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.078 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.020 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.044 2.00e-02 2.50e+03   3.41e-02 3.49e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.054 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.31: 385
        2.31 -     2.89: 5227
        2.89 -     3.46: 5498
        3.46 -     4.03: 7292
        4.03 -     4.60: 10662
  Nonbonded interactions: 29064
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.743 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.789 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.810 1.730
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.811 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.825 1.850
  ... (remaining 29059 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: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 97
        1.23 -     1.43: 375
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.54e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.36e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.26e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.78e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.57e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      102.07 -   107.59: 468
      107.59 -   113.11: 2295
      113.11 -   118.64: 393
      118.64 -   124.16: 825
      124.16 -   129.69: 98
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.22    4.38 1.00e+00 1.00e+00 1.92e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.69   -5.29 1.40e+00 5.10e-01 1.43e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.75    4.45 1.30e+00 5.92e-01 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.43: 949
       16.43 -    32.86: 53
       32.86 -    49.29: 21
       49.29 -    65.72: 8
       65.72 -    82.14: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.41   18.59     0      5.00e+00 4.00e-02 1.38e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.34   15.66     0      5.00e+00 4.00e-02 9.81e+00
  dihedral model="   0" pdb=" CB  GLU A  32 " segid="A   "
           model="   0" pdb=" CG  GLU A  32 " segid="A   "
           model="   0" pdb=" CD  GLU A  32 " segid="A   "
           model="   0" pdb=" OE1 GLU A  32 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.14   82.14     1      3.00e+01 1.11e-03 9.21e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 71
       0.049 -    0.098: 52
       0.098 -    0.147: 40
       0.147 -    0.195: 12
       0.195 -    0.244: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality model="   0" pdb=" CA  PRO A 117 " segid="A   "
            model="   0" pdb=" N   PRO A 117 " segid="A   "
            model="   0" pdb=" C   PRO A 117 " segid="A   "
            model="   0" pdb=" CB  PRO A 117 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.12e-01
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.68e-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 " segid="A   "   -0.101 2.00e-02 2.50e+03   4.24e-02 5.40e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.067 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.062 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.029 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "    0.034 2.00e-02 2.50e+03   4.23e-02 5.36e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.107 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.069 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.020 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.059 2.00e-02 2.50e+03   3.20e-02 3.07e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.038 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 304
        2.29 -     2.87: 5136
        2.87 -     3.44: 5558
        3.44 -     4.02: 7395
        4.02 -     4.60: 10917
  Nonbonded interactions: 29310
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.709 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.768 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.800 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.800 1.850
  ... (remaining 29305 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: 1.17 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 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=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.01e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.62e+00
  bond model="   0" pdb=" CB  THR A  82 " segid="A   "
       model="   0" pdb=" OG1 THR A  82 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.433  1.393  0.040 1.60e-02 3.91e+03 6.38e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.19e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.15e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.34 -   106.12: 115
      106.12 -   111.90: 2468
      111.90 -   117.68: 493
      117.68 -   123.45: 837
      123.45 -   129.23: 166
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.30    4.30 1.00e+00 1.00e+00 1.85e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.58    4.02 1.00e+00 1.00e+00 1.62e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.63    3.97 1.00e+00 1.00e+00 1.58e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.23   -4.83 1.40e+00 5.10e-01 1.19e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 942
       16.01 -    32.02: 60
       32.02 -    48.04: 24
       48.04 -    64.05: 4
       64.05 -    80.06: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.62   22.38     0      5.00e+00 4.00e-02 2.00e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.41   15.59     0      5.00e+00 4.00e-02 9.72e+00
  dihedral model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" CB  THR A  83 " segid="A   "
           model="   0" pdb=" OG1 THR A  83 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    1.26   58.74     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 69
       0.048 -    0.095: 60
       0.095 -    0.143: 36
       0.143 -    0.190: 10
       0.190 -    0.238: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.10e-01
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.40e-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 " segid="A   "    0.070 2.00e-02 2.50e+03   3.18e-02 3.03e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.058 2.00e-02 2.50e+03   3.15e-02 2.97e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.047 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "   -0.061 2.00e-02 2.50e+03   2.50e-02 1.87e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 286
        2.28 -     2.86: 5059
        2.86 -     3.44: 5591
        3.44 -     4.02: 7368
        4.02 -     4.60: 10771
  Nonbonded interactions: 29075
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.700 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.745 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.796 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.811 1.850
  ... (remaining 29070 not shown)

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

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


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


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=  2.582)
  Mean delta:    0.013 (Z=  0.657)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.632 (Z=  3.910)
  Mean delta:    1.774 (Z=  0.979)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   77.667
  Mean delta:   13.221

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.245
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.082
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.468
    Angle     :  1.651   7.632   4079  Z= 0.730
    Chirality :  0.082   0.245    176
    Planarity :  0.010   0.063    327
    Dihedral  : 11.845  79.922    769
    Min Nonbonded Distance : 1.714
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      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: -1.01 (0.68), residues: 137
    helix: -1.00 (0.47), residues: 87
    sheet: -1.96 (1.42), residues: 10
    loop :  1.12 (1.11), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.004   HIS A  43 
   PHE   0.048   0.009   PHE A  67 
   TYR   0.124   0.018   TYR A  50 
   ARG   0.071   0.015   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.004   HIS A  43 
   PHE   0.033   0.008   PHE A  67 
   TYR   0.095   0.020   TYR A  50 
   ARG   0.005   0.002   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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

  Ramachandran outliers =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.65
  MolProbity score      =   0.80

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=  2.630)
  Mean delta:    0.013 (Z=  0.653)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.96     4.64  1.00e+00  2.15e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.19     4.41  1.00e+00  1.94e+01   4.4*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    8.139 (Z=  4.639)
  Mean delta:    1.797 (Z=  0.994)

                      ----------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   156.67    23.33  5.00e+00  2.18e+01   4.7*sigma

  Min. delta:    0.016
  Max. delta:   79.218
  Mean delta:   13.230

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.240
  Mean delta:    0.084

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.079
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.465
    Angle     :  1.652   8.139   4079  Z= 0.735
    Chirality :  0.084   0.240    176
    Planarity :  0.011   0.060    327
    Dihedral  : 11.998  79.974    769
    Min Nonbonded Distance : 1.724
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      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: -0.99 (0.68), residues: 137
    helix: -0.99 (0.46), residues: 89
    sheet: -1.36 (1.52), residues: 10
    loop :  1.06 (1.19), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.005   HIS A  43 
   PHE   0.034   0.010   PHE A  67 
   TYR   0.110   0.021   TYR A  50 
   ARG   0.065   0.018   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.005   HIS A  43 
   PHE   0.021   0.006   PHE A  67 
   TYR   0.085   0.023   TYR A  91 
   ARG   0.007   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.65
  MolProbity score      =   0.95

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: ""

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


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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  3.175)
  Mean delta:    0.013 (Z=  0.664)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.889 (Z=  3.992)
  Mean delta:    1.768 (Z=  0.974)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.011
  Max. delta:   79.311
  Mean delta:   12.735

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.243
  Mean delta:    0.088

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.188
  Mean delta:    0.019

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2242  Z= 0.473
    Angle     :  1.653   7.889   4079  Z= 0.729
    Chirality :  0.088   0.243    176
    Planarity :  0.013   0.146    327
    Dihedral  : 11.613  89.978    769
    Min Nonbonded Distance : 1.715
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  1.61 %
      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: -1.79 (0.65), residues: 137
    helix: -1.34 (0.44), residues: 91
    sheet: -2.40 (1.43), residues: 10
    loop :  0.33 (1.17), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.043   0.009   PHE A  67 
   TYR   0.074   0.016   TYR A  12 
   ARG   0.154   0.030   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.029   0.009   PHE A  67 
   TYR   0.063   0.017   TYR A  12 
   ARG   0.007   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   1.19

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.037 (Z=  2.695)
  Mean delta:    0.013 (Z=  0.654)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.78     4.82  1.00e+00  2.32e+01   4.8*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.32     4.28  1.00e+00  1.83e+01   4.3*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.812 (Z=  4.816)
  Mean delta:    1.782 (Z=  0.989)

                      ----------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   140.33    39.67  5.00e+00  6.29e+01   7.9*sigma

  Min. delta:    0.028
  Max. delta:   78.132
  Mean delta:   12.864

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.232
  Mean delta:    0.081

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.104
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.465
    Angle     :  1.658   7.812   4079  Z= 0.736
    Chirality :  0.081   0.232    176
    Planarity :  0.010   0.080    327
    Dihedral  : 11.596  78.132    769
    Min Nonbonded Distance : 1.695
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  2.42 %
      Favored  : 97.58 %
    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: -0.84 (0.72), residues: 137
    helix: -0.99 (0.47), residues: 90
    sheet: -1.07 (1.74), residues: 10
    loop :  1.48 (1.28), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.042   0.008   PHE A  67 
   TYR   0.068   0.017   TYR A 111 
   ARG   0.089   0.019   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.028   0.007   PHE A  67 
   TYR   0.057   0.017   TYR A 111 
   ARG   0.003   0.001   ARG A 129 

                     ----------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: ""

============================== 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=  2.735)
  Mean delta:    0.013 (Z=  0.667)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 129  ARG  NE
   A 129  ARG  CZ
   A 129  ARG  NH2       119.20   123.37    -4.17  9.00e-01  2.14e+01   4.6*sigma
   A 129  ARG  NH1
   A 129  ARG  CZ
   A 129  ARG  NH2       119.30   113.86     5.44  1.30e+00  1.75e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.53     4.07  1.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.200 (Z=  4.630)
  Mean delta:    1.803 (Z=  0.996)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   153.03    26.97  5.00e+00  2.91e+01   5.4*sigma

  Min. delta:    0.007
  Max. delta:   77.086
  Mean delta:   13.051

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.248
  Mean delta:    0.084

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.475
    Angle     :  1.680   8.200   4079  Z= 0.743
    Chirality :  0.084   0.248    176
    Planarity :  0.010   0.070    327
    Dihedral  : 11.355  79.955    769
    Min Nonbonded Distance : 1.716
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    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: -1.21 (0.67), residues: 137
    helix: -1.54 (0.49), residues: 75
    sheet: -0.88 (1.74), residues: 10
    loop :  0.83 (0.90), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.059   0.010   PHE A  67 
   TYR   0.090   0.018   TYR A  68 
   ARG   0.077   0.018   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.040   0.010   PHE A  67 
   TYR   0.070   0.020   TYR A  68 
   ARG   0.004   0.002   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 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: ""
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.66
  MolProbity score      =   0.82

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.68
  MolProbity score      =   0.96

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A 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: ""
  Time building chain proxies: 1.03, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.703, 48.672, 75.038, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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=  0.003)
  Max. delta:    0.038 (Z=  2.678)
  Mean delta:    0.013 (Z=  0.656)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.89     4.71  1.00e+00  2.21e+01   4.7*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.53     4.07  1.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.052 (Z=  4.705)
  Mean delta:    1.776 (Z=  0.982)

                      ----------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   157.12    22.88  5.00e+00  2.09e+01   4.6*sigma

  Min. delta:    0.006
  Max. delta:   74.960
  Mean delta:   13.758

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.232
  Mean delta:    0.084

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.105
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.467
    Angle     :  1.654   8.052   4079  Z= 0.732
    Chirality :  0.084   0.232    176
    Planarity :  0.010   0.081    327
    Dihedral  : 12.590  80.008    769
    Min Nonbonded Distance : 1.740
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.84 %
      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: -1.41 (0.68), residues: 137
    helix: -1.44 (0.43), residues: 92
    sheet: -1.14 (1.63), residues: 10
    loop :  1.42 (1.29), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.033   0.007   PHE A  67 
   TYR   0.080   0.015   TYR A  12 
   ARG   0.089   0.019   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.022   0.007   PHE A  67 
   TYR   0.066   0.016   TYR A  12 
   ARG   0.006   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.65
  MolProbity score      =   0.82

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=  2.670)
  Mean delta:    0.013 (Z=  0.657)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.39     4.21  1.00e+00  1.77e+01   4.2*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   116.74    -4.14  1.00e+00  1.72e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.143 (Z=  4.208)
  Mean delta:    1.795 (Z=  0.999)

                      ----------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  -151.76   -28.24  5.00e+00  3.19e+01   5.6*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   159.60    20.40  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.001
  Max. delta:   76.677
  Mean delta:   13.915

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.235
  Mean delta:    0.087

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.081
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.669   8.143   4079  Z= 0.743
    Chirality :  0.087   0.235    176
    Planarity :  0.010   0.065    327
    Dihedral  : 12.233  76.677    769
    Min Nonbonded Distance : 1.727
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.84 %
      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: -1.53 (0.68), residues: 137
    helix: -1.10 (0.48), residues: 90
    sheet: -2.28 (1.28), residues: 10
    loop :  0.24 (1.17), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.003   HIS A  43 
   PHE   0.047   0.010   PHE A  67 
   TYR   0.145   0.020   TYR A  91 
   ARG   0.066   0.019   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.003   HIS A  43 
   PHE   0.032   0.009   PHE A  67 
   TYR   0.121   0.022   TYR A  91 
   ARG   0.017   0.003   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.67
  MolProbity score      =   0.90

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}

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


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


============================== 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: 1.21, per 1000 atoms: 0.55
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.833, 56.606, 64.923, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (79.493, 44.125, 43.828, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

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


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

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.69, 53.263, 55.434, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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:    0.038 (Z=  2.650)
  Mean delta:    0.013 (Z=  0.657)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.79     4.81  1.00e+00  2.32e+01   4.8*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   131.02    -6.62  1.40e+00  2.24e+01   4.7*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.80     5.40  1.30e+00  1.73e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.379 (Z=  4.814)
  Mean delta:    1.811 (Z=  1.007)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.033
  Max. delta:   77.351
  Mean delta:   13.334

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.308
  Mean delta:    0.088

                       ----------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            0.062       0.117       76.83   5.8*sigma

  Min. delta:    0.000
  Max. delta:    0.064
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.676   7.379   4079  Z= 0.746
    Chirality :  0.088   0.308    176
    Planarity :  0.010   0.056    327
    Dihedral  : 12.221  83.194    769
    Min Nonbonded Distance : 1.758
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      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: -1.36 (0.67), residues: 137
    helix: -1.47 (0.43), residues: 93
    sheet: -1.92 (1.60), residues: 10
    loop :  2.04 (1.19), residues: 34
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.046   0.009   PHE A  67 
   TYR   0.137   0.023   TYR A  81 
   ARG   0.057   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.031   0.008   PHE A  67 
   TYR   0.117   0.022   TYR A  81 
   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 ==============================


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=  2.758)
  Mean delta:    0.013 (Z=  0.658)

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

   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=  2.672)
  Mean delta:    0.013 (Z=  0.664)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.90     4.70  1.00e+00  2.20e+01   4.7*sigma
   A 124  ALA  N
   A 124  ALA  CA
   A 124  ALA  CB        110.40   103.62     6.78  1.50e+00  2.04e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.30     4.30  1.00e+00  1.85e+01   4.3*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.06    -5.66  1.40e+00  1.63e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.000)
  Max. delta:    7.937 (Z=  4.695)
  Mean delta:    1.817 (Z=  1.006)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   77.771
  Mean delta:   12.472

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.258
  Mean delta:    0.085

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.054       0.106       58.51   5.3*sigma

  Min. delta:    0.000
  Max. delta:    0.073
  Mean delta:    0.014

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


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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.82     4.78  1.00e+00  2.28e+01   4.8*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.21     5.99  1.30e+00  2.12e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.25     4.35  1.00e+00  1.89e+01   4.3*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.78     5.42  1.30e+00  1.74e+01   4.2*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    8.154 (Z=  4.780)
  Mean delta:    1.803 (Z=  0.996)

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

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

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

  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   150.38    29.62  5.00e+00  3.51e+01   5.9*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   153.35    26.65  5.00e+00  2.84e+01   5.3*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   155.20    24.80  5.00e+00  2.46e+01   5.0*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   158.97    21.03  5.00e+00  1.77e+01   4.2*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   159.87    20.13  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.005
  Max. delta:   78.113
  Mean delta:   13.221

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.234
  Mean delta:    0.083

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.670   7.937   4079  Z= 0.744
    Chirality :  0.085   0.258    176
    Planarity :  0.010   0.059    327
    Dihedral  : 11.273  77.771    769
    Min Nonbonded Distance : 1.723
  
  Molprobity Statistics.
    All-atom Clashscore : 2.25
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    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: -1.59 (0.64), residues: 137
    helix: -1.29 (0.46), residues: 85
    sheet: -2.54 (1.07), residues: 10
    loop :  0.46 (1.02), residues: 42
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.005   HIS A  43 
   PHE   0.052   0.011   PHE A  67 
   TYR   0.149   0.021   TYR A  50 
   ARG   0.063   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.005   HIS A  43 
   PHE   0.036   0.009   PHE A  67 
   TYR   0.107   0.023   TYR A  91 
   ARG   0.004   0.001   ARG A  58 

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

   A 136  HIS

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.047       0.081       44.42   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.067
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.472
    Angle     :  1.664   8.154   4079  Z= 0.739
    Chirality :  0.083   0.234    176
    Planarity :  0.009   0.052    327
    Dihedral  : 12.231  80.003    769
    Min Nonbonded Distance : 1.732
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  6.57 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  4.03 %
      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: -2.78 (0.64), residues: 137
    helix: -2.47 (0.40), residues: 80
    sheet: -1.39 (1.56), residues: 10
    loop : -0.25 (1.04), residues: 47
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.004   HIS A 136 
   PHE   0.045   0.009   PHE A  67 
   TYR   0.101   0.016   TYR A  91 
   ARG   0.058   0.012   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.004   HIS A 136 
   PHE   0.031   0.008   PHE A  67 
   TYR   0.081   0.017   TYR A  91 
   ARG   0.005   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  94.89 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   2.25
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.67
  MolProbity score      =   1.36

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.19 %
                favored =  91.24 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   1.80
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   1.45

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.68
  MolProbity score      =   1.12

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

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


  Symmetric amino acids flipped
    Residue "A 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: ""

============================== 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=  2.751)
  Mean delta:    0.013 (Z=  0.661)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.80     4.80  1.00e+00  2.31e+01   4.8*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.91     5.29  1.30e+00  1.66e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.396 (Z=  4.805)
  Mean delta:    1.788 (Z=  0.986)

                      ----------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   148.86    31.14  5.00e+00  3.88e+01   6.2*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   153.82    26.18  5.00e+00  2.74e+01   5.2*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   157.50    22.50  5.00e+00  2.03e+01   4.5*sigma

  Min. delta:    0.052
  Max. delta:   77.288
  Mean delta:   13.542

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:    0.232
  Mean delta:    0.084

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.111
  Mean delta:    0.016

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


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

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

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

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

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

    1" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    1" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    1" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    1" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    1" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    1" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    1" pdbres="HIS A 139 " segid="A    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= 0.471
    Angle     :  1.663   7.396   4079  Z= 0.735
    Chirality :  0.084   0.232    176
    Planarity :  0.011   0.085    327
    Dihedral  : 12.723  88.514    769
    Min Nonbonded Distance : 1.705
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    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 : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.10 (0.66), residues: 137
    helix: -2.01 (0.45), residues: 83
    sheet: -1.75 (1.45), residues: 10
    loop :  0.58 (1.03), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.082   0.013   PHE A  67 
   TYR   0.087   0.019   TYR A  81 
   ARG   0.092   0.021   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.057   0.013   PHE A  67 
   TYR   0.073   0.020   TYR A  81 
   ARG   0.005   0.002   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)----------                  

  Ramachandran outliers =   0.00 %
                favored =  94.89 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   1.17

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

============================== 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: 0.91
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.03 seconds

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


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:    0.045 (Z=  2.830)
  Mean delta:    0.013 (Z=  0.660)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.84     4.76  1.00e+00  2.27e+01   4.8*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.19     4.41  1.00e+00  1.95e+01   4.4*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.882 (Z=  4.762)
  Mean delta:    1.775 (Z=  0.983)

                      ----------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   157.15    22.85  5.00e+00  2.09e+01   4.6*sigma

  Min. delta:    0.013
  Max. delta:   76.811
  Mean delta:   14.145

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.234
  Mean delta:    0.083

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.104
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.045   2242  Z= 0.470
    Angle     :  1.652   7.882   4079  Z= 0.732
    Chirality :  0.083   0.234    176
    Planarity :  0.011   0.080    327
    Dihedral  : 12.824  80.070    769
    Min Nonbonded Distance : 1.722
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    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: -1.47 (0.66), residues: 137
    helix: -1.26 (0.44), residues: 91
    sheet: -2.92 (1.14), residues: 10
    loop :  1.24 (1.18), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.038   0.008   PHE A  67 
   TYR   0.091   0.016   TYR A  91 
   ARG   0.086   0.019   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.025   0.007   PHE A  67 
   TYR   0.077   0.017   TYR A  91 
   ARG   0.005   0.002   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.639)
  Mean delta:    0.013 (Z=  0.664)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.20     4.40  1.00e+00  1.94e+01   4.4*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.758 (Z=  4.399)
  Mean delta:    1.773 (Z=  0.983)

                      ----------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   149.02    30.98  5.00e+00  3.84e+01   6.2*sigma

  Min. delta:    0.011
  Max. delta:   79.684
  Mean delta:   12.822

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.228
  Mean delta:    0.084

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.082
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.473
    Angle     :  1.657   7.758   4079  Z= 0.733
    Chirality :  0.084   0.228    176
    Planarity :  0.010   0.062    327
    Dihedral  : 11.761  79.684    769
    Min Nonbonded Distance : 1.700
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.43 (0.68), residues: 137
    helix: -1.48 (0.46), residues: 87
    sheet: -0.86 (1.68), residues: 10
    loop :  0.96 (1.10), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.004   HIS A  43 
   PHE   0.051   0.010   PHE A  67 
   TYR   0.084   0.017   TYR A  68 
   ARG   0.071   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.004   HIS A  43 
   PHE   0.034   0.010   PHE A  67 
   TYR   0.065   0.017   TYR A  68 
   ARG   0.005   0.001   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   0.95

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: 64
        1.23 -     1.42: 408
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.00e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.73e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.70e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.06e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.01e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.33 -   106.11: 116
      106.11 -   111.89: 2460
      111.89 -   117.68: 500
      117.68 -   123.46: 839
      123.46 -   129.25: 164
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.60    4.00 1.00e+00 1.00e+00 1.60e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" C   LYS A  85 " segid="A   "
        model="   0" pdb=" N   ILE A  86 " segid="A   "
        model="   0" pdb=" CA  ILE A  86 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.70  128.10   -6.40 1.80e+00 3.09e-01 1.26e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 950
       16.01 -    32.01: 54
       32.01 -    48.02: 20
       48.02 -    64.02: 6
       64.02 -    80.03: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  dihedral model="   0" pdb=" CA  VAL A 112 " segid="A   "
           model="   0" pdb=" C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.60   15.40     0      5.00e+00 4.00e-02 9.49e+00
  dihedral model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
           model="   0" pdb=" CB  HIS A 139 " segid="A   "
           model="   0" pdb=" CG  HIS A 139 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.54  -58.46     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 72
       0.046 -    0.092: 53
       0.092 -    0.137: 36
       0.137 -    0.183: 14
       0.183 -    0.228: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.53e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 6.93e-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 " segid="A   "    0.060 2.00e-02 2.50e+03   4.17e-02 5.22e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.081 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.059 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.053 2.00e-02 2.50e+03   3.40e-02 3.47e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.057 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.072 2.00e-02 2.50e+03   3.18e-02 3.04e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.28: 295
        2.28 -     2.86: 5103
        2.86 -     3.44: 5518
        3.44 -     4.02: 7274
        4.02 -     4.60: 10704
  Nonbonded interactions: 28894
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.705 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.771 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.774 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.791 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.800 1.730
  ... (remaining 28889 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   0.90

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)----------                  

  Time building chain proxies: 0.74, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.669, 47.287, 39.488, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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=  2.714)
  Mean delta:    0.012 (Z=  0.623)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  52  PRO  C
   A  53  LEU  N
   A  53  LEU  CA        121.70   129.43    -7.73  1.80e+00  1.84e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.048 (Z=  4.295)
  Mean delta:    1.757 (Z=  0.976)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.013
  Max. delta:   89.325
  Mean delta:   15.490

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.227
  Mean delta:    0.081

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.069
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.444
    Angle     :  1.639   8.048   4079  Z= 0.727
    Chirality :  0.081   0.227    176
    Planarity :  0.010   0.056    327
    Dihedral  : 13.404  89.325    769
    Min Nonbonded Distance : 1.749
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  1.61 %
      Favored  : 96.77 %
    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: -2.85 (0.62), residues: 137
    helix: -2.04 (0.45), residues: 79
    sheet: -3.28 (0.99), residues: 10
    loop : -0.83 (0.93), residues: 48
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.006   HIS A  43 
   PHE   0.034   0.008   PHE A  67 
   TYR   0.139   0.019   TYR A  50 
   ARG   0.060   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.006   HIS A  43 
   PHE   0.024   0.007   PHE A  67 
   TYR   0.107   0.022   TYR A  50 
   ARG   0.006   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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


End of input processing

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

   Number of:
     all atoms      : 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=  2.702)
  Mean delta:    0.013 (Z=  0.664)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.156 (Z=  4.088)
  Mean delta:    1.743 (Z=  0.968)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.032
  Max. delta:   79.675
  Mean delta:   11.325

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.236
  Mean delta:    0.080

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A 118  ASP  CB
   A 118  ASP  CG
   A 118  ASP  OD1
   A 118  ASP  OD2           0.057       0.099       32.99   5.0*sigma

  Min. delta:    0.000
  Max. delta:    0.099
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.473
    Angle     :  1.634   7.156   4079  Z= 0.723
    Chirality :  0.080   0.236    176
    Planarity :  0.011   0.076    327
    Dihedral  : 10.643  79.675    769
    Min Nonbonded Distance : 1.718
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    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: -1.03 (0.68), residues: 137
    helix: -1.43 (0.50), residues: 76
    sheet: -0.33 (1.60), residues: 10
    loop :  0.92 (0.93), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A  43 
   PHE   0.027   0.006   PHE A  67 
   TYR   0.071   0.018   TYR A  12 
   ARG   0.085   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A  43 
   PHE   0.022   0.006   PHE A  67 
   TYR   0.060   0.021   TYR A  12 
   ARG   0.004   0.001   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 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 =  94.16 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   1.80
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.64
  MolProbity score      =   1.49

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.63
  MolProbity score      =   0.82

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.037 (Z=  3.097)
  Mean delta:    0.012 (Z=  0.637)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.740 (Z=  3.963)
  Mean delta:    1.650 (Z=  0.913)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.004
  Max. delta:   93.697
  Mean delta:   11.861

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:    0.234
  Mean delta:    0.077

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.079
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.454
    Angle     :  1.576   8.740   4079  Z= 0.691
    Chirality :  0.077   0.234    176
    Planarity :  0.010   0.064    327
    Dihedral  : 11.051  93.697    769
    Min Nonbonded Distance : 1.719
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.73 %
      Favored  : 99.27 %
    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: -1.03 (0.69), residues: 137
    helix: -1.48 (0.48), residues: 76
    sheet: -1.39 (1.54), residues: 10
    loop :  1.28 (0.97), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.005   HIS A  43 
   PHE   0.049   0.008   PHE A  67 
   TYR   0.081   0.016   TYR A  50 
   ARG   0.065   0.017   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.020   0.005   HIS A  43 
   PHE   0.034   0.008   PHE A  67 
   TYR   0.065   0.016   TYR A  50 
   ARG   0.006   0.002   ARG A 129 

                     ----------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:    0.038 (Z=  2.673)
  Mean delta:    0.013 (Z=  0.658)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.76     4.84  1.00e+00  2.34e+01   4.8*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.54     5.66  1.30e+00  1.89e+01   4.4*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.191 (Z=  4.841)
  Mean delta:    1.791 (Z=  0.986)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   138.95    41.05  5.00e+00  6.74e+01   8.2*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   150.37    29.63  5.00e+00  3.51e+01   5.9*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   155.71    24.29  5.00e+00  2.36e+01   4.9*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   156.60    23.40  5.00e+00  2.19e+01   4.7*sigma

  Min. delta:    0.031
  Max. delta:   78.038
  Mean delta:   12.752

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.225
  Mean delta:    0.082

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.099       0.083      196.55   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.099
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.657   8.191   4079  Z= 0.733
    Chirality :  0.082   0.225    176
    Planarity :  0.011   0.092    327
    Dihedral  : 11.478  78.038    769
    Min Nonbonded Distance : 1.727
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  4.38 %
      Favored  : 93.43 %
    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 : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.30 (0.67), residues: 137
    helix: -1.98 (0.45), residues: 79
    sheet: -1.70 (1.52), residues: 10
    loop : -0.20 (1.06), residues: 48
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.003   HIS A  43 
   PHE   0.042   0.009   PHE A  67 
   TYR   0.220   0.023   TYR A  50 
   ARG   0.071   0.016   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.003   HIS A  43 
   PHE   0.029   0.008   PHE A  67 
   TYR   0.182   0.026   TYR A  50 
   ARG   0.004   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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


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

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

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

  Ramachandran outliers =   0.00 %
                favored =  99.27 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.58
  MolProbity score      =   0.50

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.19 %
                favored =  93.43 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.66
  MolProbity score      =   1.25

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)----------                  


  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: 1.11
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.24 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: 1.23
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.38 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 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.

  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=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.98e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.97e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.39e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.30e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.29e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.11 -   105.92: 94
      105.92 -   111.73: 2434
      111.73 -   117.53: 543
      117.53 -   123.34: 835
      123.34 -   129.15: 173
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.07    4.53 1.00e+00 1.00e+00 2.05e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.07    4.53 1.00e+00 1.00e+00 2.05e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.82    3.78 1.00e+00 1.00e+00 1.43e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.37    4.83 1.30e+00 5.92e-01 1.38e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.39    4.81 1.30e+00 5.92e-01 1.37e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 963
       17.99 -    35.98: 52
       35.98 -    53.97: 15
       53.97 -    71.96: 1
       71.96 -    89.96: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 " segid="A   "
           model="   0" pdb=" C   ASP A 118 " segid="A   "
           model="   0" pdb=" N   LEU A 119 " segid="A   "
           model="   0" pdb=" CA  LEU A 119 " segid="A   "
      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  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.00   18.00     0      5.00e+00 4.00e-02 1.30e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.34   16.66     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.053: 76
       0.053 -    0.105: 62
       0.105 -    0.157: 32
       0.157 -    0.208: 4
       0.208 -    0.260: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality model="   0" pdb=" CA  PRO A 117 " segid="A   "
            model="   0" pdb=" N   PRO A 117 " segid="A   "
            model="   0" pdb=" C   PRO A 117 " segid="A   "
            model="   0" pdb=" CB  PRO A 117 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    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 111 " segid="A   "    0.062 2.00e-02 2.50e+03   3.70e-02 4.10e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.041 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.048 2.00e-02 2.50e+03   3.67e-02 4.04e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.095 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.051 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane mo
  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: ""
del="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.019 2.00e-02 2.50e+03   2.67e-02 2.14e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 314
        2.29 -     2.87: 5128
        2.87 -     3.44: 5491
        3.44 -     4.02: 7240
        4.02 -     4.60: 10586
  Nonbonded interactions: 28759
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.712 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.745 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.800 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.803 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.804 1.730
  ... (remaining 28754 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: 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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.20e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.65e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.60e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.28e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.79e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.77 -   105.67: 79
      105.67 -   111.58: 2400
      111.58 -   117.48: 584
      117.48 -   123.39: 845
      123.39 -   129.29: 171
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.21    4.39 1.00e+00 1.00e+00 1.92e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.19    5.01 1.30e+00 5.92e-01 1.48e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.29   -4.89 1.40e+00 5.10e-01 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.32: 940
       15.32 -    30.65: 59
       30.65 -    45.97: 22
       45.97 -    61.29: 10
       61.29 -    76.62: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.57   18.43     0      5.00e+00 4.00e-02 1.36e+01
  dihedral model="   0" pdb=" CA  ILE A  86 " segid="A   "
           model="   0" pdb=" C   ILE A  86 " segid="A   "
           model="   0" pdb=" N   GLY A  87 " segid="A   "
           model="   0" pdb=" CA  GLY A  87 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.17   16.83     0      5.00e+00 4.00e-02 1.13e+01
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.58   16.42     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 68
       0.049 -    0.097: 62
       0.097 -    0.145: 36
       0.145 -    0.193: 9
       0.193 -    0.241: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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 " segid="A   "
            model="   0" pdb=" N   ILE A  86 " segid="A   "
            model="   0" pdb=" C   ILE A  86 " segid="A   "
            model="   0" pdb=" CB  ILE A  86 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.96e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.16 2.00e-01 2.50e+01 6.74e-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 " segid="A   "   -0.071 2.00e-02 2.50e+03   3.51e-02 3.69e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.069 2.00e-02 2.50e+03   3.08e-02 2.85e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.064 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.028 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  67 " segid="A   "   -0.068 2.00e-02 2.50e+03   2.59e-02 2.02e+01
        model="   0" pdb=" CG  PHE A  67 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  67 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  67 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  67 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  67 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  67 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  67 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  67 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  67 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  67 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  67 " segid="A   "   -0.026 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 300
        2.28 -     2.86: 5083
        2.86 -     3.44: 5585
        3.44 -     4.02: 7340
        4.02 -     4.60: 10876
  Nonbonded interactions: 29184
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.704 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.748 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.777 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.809 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.824 1.850
  ... (remaining 29179 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: 75
        1.23 -     1.43: 397
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.70e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.04e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.80e+00
  bond model="   0" pdb=" CE1 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    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=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.399 -0.025 1.10e-02 8.26e+03 5.35e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.08 -   105.89: 114
      105.89 -   111.71: 2409
      111.71 -   117.53: 561
      117.53 -   123.35: 809
      123.35 -   129.17: 186
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 138 " segid="A   "
        model="   0" pdb=" CG  HIS A 138 " segid="A   "
        model="   0" pdb=" CD2 HIS A 138 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.38    5.82 1.30e+00 5.92e-01 2.00e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.20    4.40 1.00e+00 1.00e+00 1.93e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CA  HIS A 138 " segid="A   "
        model="   0" pdb=" CB  HIS A 138 " segid="A   "
        model="   0" pdb=" CG  HIS A 138 " segid="A   "
      ideal   model   delta    sigma   weight residual
     113.80  110.04    3.76 1.00e+00 1.00e+00 1.41e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 953
       17.99 -    35.99: 58
       35.99 -    53.98: 18
       53.98 -    71.98: 1
       71.98 -    89.97: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 135 " segid="A   "
           model="   0" pdb=" C   HIS A 135 " segid="A   "
           model="   0" pdb=" N   HIS A 136 " segid="A   "
           model="   0" pdb=" CA  HIS A 136 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.67   36.33     0      5.00e+00 4.00e-02 5.28e+01
  dihedral model="   0" pdb=" CA  HIS A 136 " segid="A   "
           model="   0" pdb=" C   HIS A 136 " segid="A   "
           model="   0" pdb=" N   HIS A 137 " segid="A   "
           model="   0" pdb=" CA  HIS A 137 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.45   35.55     0      5.00e+00 4.00e-02 5.06e+01
  dihedral model="   0" pdb=" CA  MET A 128 " segid="A   "
           model="   0" pdb=" C   MET A 128 " segid="A   "
           model="   0" pdb=" N   ARG A 129 " segid="A   "
           model="   0" pdb=" CA  ARG A 129 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.66   32.34     0      5.00e+00 4.00e-02 4.18e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.062: 89
       0.062 -    0.124: 60
       0.124 -    0.185: 23
       0.185 -    0.247: 3
       0.247 -    0.308: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A 122 " segid="A   "
            model="   0" pdb=" N   ILE A 122 " segid="A   "
            model="   0" pdb=" C   ILE A 122 " segid="A   "
            model="   0" pdb=" CB  ILE A 122 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.13    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.089 2.00e-02 2.50e+03   3.98e-02 4.75e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.082 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03   3.45e-02 3.58e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.051 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.074 2.00e-02 2.50e+03   2.94e-02 2.59e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 359
        2.30 -     2.88: 5214
        2.88 -     3.45: 5400
        3.45 -     4.03: 7198
        4.03 -     4.60: 10559
  Nonbonded interactions: 28730
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.731 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.783 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.795 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.809 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.812 1.850
  ... (remaining 28725 not shown)

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

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

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

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
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=  2.685)
  Mean delta:    0.013 (Z=  0.646)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.13     6.07  1.30e+00  2.18e+01   4.7*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.07     4.53  1.00e+00  2.05e+01   4.5*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.63    -6.23  1.40e+00  1.98e+01   4.5*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   116.86    -4.26  1.00e+00  1.82e+01   4.3*sigma
   A  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:    0.002 (Z=  0.001)
  Max. delta:    7.969 (Z=  4.669)
  Mean delta:    1.783 (Z=  1.010)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   89.300
  Mean delta:   13.700

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.246
  Mean delta:    0.084

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.099
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.460
    Angle     :  1.652   7.969   4079  Z= 0.745
    Chirality :  0.084   0.246    176
    Planarity :  0.011   0.076    327
    Dihedral  : 12.631  89.948    769
    Min Nonbonded Distance : 1.744
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    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: -2.00 (0.63), residues: 137
    helix: -1.91 (0.46), residues: 76
    sheet:  None (None), residues: 0
    loop : -0.26 (0.80), residues: 61
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.005   HIS A  43 
   PHE   0.074   0.012   PHE A  67 
   TYR   0.118   0.024   TYR A  91 
   ARG   0.082   0.016   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.005   HIS A  43 
   PHE   0.051   0.013   PHE A  67 
   TYR   0.075   0.021   TYR A  12 
   ARG   0.005   0.001   ARG A  58 

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

   A  66  GLN

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.702)
  Mean delta:    0.013 (Z=  0.656)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.11     4.49  1.00e+00  2.02e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.33     4.27  1.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.985 (Z=  4.493)
  Mean delta:    1.820 (Z=  0.997)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   76.300
  Mean delta:   12.511

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.254
  Mean delta:    0.084

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.082
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.467
    Angle     :  1.677   7.985   4079  Z= 0.741
    Chirality :  0.084   0.254    176
    Planarity :  0.011   0.063    327
    Dihedral  : 11.544  80.034    769
    Min Nonbonded Distance : 1.697
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    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: -0.98 (0.72), residues: 137
    helix: -1.20 (0.46), residues: 92
    sheet: -1.04 (1.64), residues: 10
    loop :  1.90 (1.35), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.048   0.009   PHE A  67 
   TYR   0.092   0.018   TYR A  68 
   ARG   0.071   0.022   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.032   0.008   PHE A  67 
   TYR   0.074   0.018   TYR A  12 
   ARG   0.007   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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

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

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


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


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

  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.68
  MolProbity score      =   1.08

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0090
  RMS(angles)           =   1.65
  MolProbity score      =   0.96

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: ""
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.096, 56.121, 56.584, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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:    0.043 (Z=  2.695)
  Mean delta:    0.013 (Z=  0.669)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.778 (Z=  4.123)
  Mean delta:    1.766 (Z=  0.971)

                      ----------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   158.07    21.93  5.00e+00  1.92e+01   4.4*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   158.99    21.01  5.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.008
  Max. delta:   77.883
  Mean delta:   12.521

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.292
  Mean delta:    0.085

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.082
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.043   2242  Z= 0.476
    Angle     :  1.648   7.778   4079  Z= 0.726
    Chirality :  0.085   0.292    176
    Planarity :  0.010   0.062    327
    Dihedral  : 11.590  77.883    769
    Min Nonbonded Distance : 1.718
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    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: -1.23 (0.69), residues: 137
    helix: -1.96 (0.47), residues: 70
    sheet: -1.13 (1.65), residues: 10
    loop :  1.23 (0.92), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.039   0.008   PHE A  67 
   TYR   0.101   0.020   TYR A  91 
   ARG   0.069   0.018   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.027   0.008   PHE A  67 
   TYR   0.084   0.023   TYR A  91 
   ARG   0.004   0.002   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}

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=  3.152)
  Mean delta:    0.013 (Z=  0.643)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  CD2       131.20   125.25     5.95  1.30e+00  2.09e+01   4.6*sigma
   A 125  LYS  CG
   A 125  LYS  CD
   A 125  LYS  CE        111.30   101.64     9.66  2.30e+00  1.77e+01   4.2*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.71e+01   4.1*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.48     4.12  1.00e+00  1.70e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.004 (Z=  0.002)
  Max. delta:    9.664 (Z=  4.574)
  Mean delta:    1.691 (Z=  0.948)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   81.958
  Mean delta:   12.617

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.226
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.078
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.458
    Angle     :  1.588   9.664   4079  Z= 0.707
    Chirality :  0.076   0.226    176
    Planarity :  0.010   0.073    327
    Dihedral  : 11.275  81.958    769
    Min Nonbonded Distance : 1.773
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    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: -0.35 (0.65), residues: 137
    helix: -0.78 (0.53), residues: 70
    sheet: -0.95 (1.44), residues: 10
    loop :  1.01 (0.79), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.005   HIS A 135 
   PHE   0.043   0.007   PHE A  67 
   TYR   0.165   0.021   TYR A  50 
   ARG   0.054   0.011   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.005   HIS A 135 
   PHE   0.030   0.006   PHE A  67 
   TYR   0.144   0.022   TYR A  50 
   ARG   0.004   0.001   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  99.27 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.59
  MolProbity score      =   0.66

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.65
  MolProbity score      =   0.82

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        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 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: ""

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

  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.586, 66.234, 61.568, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: ""

============================== 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: 1.02
  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.


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


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

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (61.087, 50.189, 42.579, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 56
        1.23 -     1.42: 416
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.52e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.27e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.82e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.20e+00
  bond model="   0" pdb=" ND1 HIS A 137 " segid="A   "
       model="   0" pdb=" CE1 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.77e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.85 -   106.29: 128
      106.29 -   112.73: 2587
      112.73 -   119.18: 505
      119.18 -   125.62: 814
      125.62 -   132.06: 45
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  132.06   -7.66 1.40e+00 5.10e-01 3.00e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.20    4.40 1.00e+00 1.00e+00 1.94e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.35    4.25 1.00e+00 1.00e+00 1.80e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.85    5.35 1.30e+00 5.92e-01 1.70e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.91    5.29 1.30e+00 5.92e-01 1.66e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.40: 962
       16.40 -    32.79: 47
       32.79 -    49.19: 14
       49.19 -    65.59: 7
       65.59 -    81.99: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.19   29.81     0      5.00e+00 4.00e-02 3.55e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.43   16.57     0      5.00e+00 4.00e-02 1.10e+01
  dihedral model="   0" pdb=" CA  ALA A 115 " segid="A   "
           model="   0" pdb=" C  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.625, 57.142, 54.316, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
   ALA A 115 " segid="A   "
           model="   0" pdb=" N   ASP A 116 " segid="A   "
           model="   0" pdb=" CA  ASP A 116 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.17   15.83     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 81
       0.057 -    0.115: 65
       0.115 -    0.172: 23
       0.172 -    0.229: 5
       0.229 -    0.286: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality model="   0" pdb=" CA  THR A  83 " segid="A   "
            model="   0" pdb=" N   THR A  83 " segid="A   "
            model="   0" pdb=" C   THR A  83 " segid="A   "
            model="   0" pdb=" CB  THR A  83 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.22 2.00e-01 2.50e+01 1.19e+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 " segid="A   "    0.043 2.00e-02 2.50e+03   4.88e-02 7.15e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.125 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.078 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.029 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.075 2.00e-02 2.50e+03   3.25e-02 3.16e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.053 2.00e-02 2.50e+03   3.12e-02 2.91e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 324
        2.30 -     2.87: 5234
        2.87 -     3.45: 5601
        3.45 -     4.02: 7486
        4.02 -     4.60: 11085
  Nonbonded interactions: 29730
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.719 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.733 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.795 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.796 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.834 1.850
  ... (remaining 29725 not shown)

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.037 (Z=  2.814)
  Mean delta:    0.013 (Z=  0.659)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.92     4.68  1.00e+00  2.19e+01   4.7*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.29     4.31  1.00e+00  1.86e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.52     4.08  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.317 (Z=  4.684)
  Mean delta:    1.809 (Z=  0.991)

                      ----------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   147.32    32.68  5.00e+00  4.27e+01   6.5*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   148.48    31.52  5.00e+00  3.97e+01   6.3*sigma

  Min. delta:    0.040
  Max. delta:   76.071
  Mean delta:   12.428

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.260
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.071
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.469
    Angle     :  1.665   8.317   4079  Z= 0.736
    Chirality :  0.082   0.260    176
    Planarity :  0.010   0.055    327
    Dihedral  : 11.176  76.071    769
    Min Nonbonded Distance : 1.722
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  6.57 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.81 %
      Favored  : 97.58 %
    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: -1.72 (0.68), residues: 137
    helix: -1.63 (0.43), residues: 88
    sheet: -1.38 (1.61), residues: 10
    loop :  0.83 (1.23), residues: 39
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.047   0.010   PHE A  67 
   TYR   0.076   0.016   TYR A  68 
   ARG   0.062   0.014   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.032   0.009   PHE A  67 
   TYR   0.062   0.017   TYR A 111 
   ARG   0.005   0.002   ARG A  58 

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

   A 137  HIS

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


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

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

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

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

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


  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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   2.19 %
                favored =  91.24 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   1.80
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   1.61

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=  2.747)
  Mean delta:    0.013 (Z=  0.658)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.22     4.38  1.00e+00  1.92e+01   4.4*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:    7.973 (Z=  4.385)
  Mean delta:    1.767 (Z=  0.977)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.047
  Max. delta:   82.144
  Mean delta:   13.162

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.244
  Mean delta:    0.086

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.041       0.082       33.79   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.071
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.653   7.973   4079  Z= 0.730
    Chirality :  0.086   0.244    176
    Planarity :  0.010   0.054    327
    Dihedral  : 12.386  82.144    769
    Min Nonbonded Distance : 1.709
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    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: -1.13 (0.69), residues: 137
    helix: -1.36 (0.45), residues: 89
    sheet: -2.14 (1.39), residues: 10
    loop :  2.02 (1.18), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.021   0.004   HIS A  43 
   PHE   0.045   0.009   PHE A  67 
   TYR   0.107   0.019   TYR A  50 
   ARG   0.058   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.021   0.004   HIS A  43 
   PHE   0.031   0.008   PHE A  67 
   TYR   0.082   0.020   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   0.82

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: ""

  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 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: (79.771, 48.205, 53.442, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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}

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

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=  2.672)
  Mean delta:    0.013 (Z=  0.661)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.19     4.41  1.00e+00  1.95e+01   4.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.24     4.36  1.00e+00  1.90e+01   4.4*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.045 (Z=  4.411)
  Mean delta:    1.797 (Z=  0.989)

                      ----------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   153.15    26.85  5.00e+00  2.88e+01   5.4*sigma

  Min. delta:    0.025
  Max. delta:   78.193
  Mean delta:   13.104

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.245
  Mean delta:    0.081

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.046       0.081       42.09   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.081
  Mean delta:    0.016

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.471
    Angle     :  1.658   7.045   4079  Z= 0.734
    Chirality :  0.081   0.245    176
    Planarity :  0.011   0.062    327
    Dihedral  : 12.066  83.238    769
    Min Nonbonded Distance : 1.743
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    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: -0.92 (0.67), residues: 137
    helix: -1.11 (0.45), residues: 85
    sheet: -0.83 (1.70), residues: 10
    loop :  1.16 (1.07), residues: 42
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.052   0.010   PHE A  67 
   TYR   0.101   0.020   TYR A  91 
   ARG   0.070   0.021   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.036   0.009   PHE A  67 
   TYR   0.081   0.022   TYR A  91 
   ARG   0.005   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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

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

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


  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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.01, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.451, 44.329, 55.077, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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 =  97.08 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   1.80
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   1.26

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.902, 42.41, 51.517, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (73.041, 46.27, 55.525, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  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.


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

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.772, 48.275, 38.988, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (72.959, 53.757, 41.081, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A 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: ""

============================== 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: ""
  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 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.54e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.04e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.73e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.72e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.82e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.07 -   105.91: 97
      105.91 -   111.75: 2447
      111.75 -   117.59: 530
      117.59 -   123.44: 849
      123.44 -   129.28: 156
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.06    4.54 1.00e+00 1.00e+00 2.06e+01
  angle model="   0" pdb=" CA  ASP A  36 " segid="A   "
        model="   0" pdb=" CB  ASP A  36 " segid="A   "
        model="   0" pdb=" CG  ASP A  36 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.92   -4.32 1.00e+00 1.00e+00 1.86e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.28   -4.88 1.40e+00 5.10e-01 1.21e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.15    3.45 1.00e+00 1.00e+00 1.19e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.95: 953
       15.95 -    31.91: 60
       31.91 -    47.86: 13
       47.86 -    63.81: 5
       63.81 -    79.77: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.00   25.00     0      5.00e+00 4.00e-02 2.50e+01
  dihedral model="   0" pdb=" CA  VAL A 112 " segid="A   "
           model="   0" pdb=" C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.51   16.49     0      5.00e+00 4.00e-02 1.09e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.76   16.24     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 69
       0.052 -    0.103: 67
       0.103 -    0.154: 35
       0.154 -    0.206: 4
       0.206 -    0.257: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    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=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 8.27e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.087 2.00e-02 2.50e+03   3.97e-02 4.72e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.083 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.036 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.082 2.00e-02 2.50e+03   3.63e-02 3.96e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.023 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.030 2.00e-02 2.50e+03   2.53e-02 1.91e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.28: 299
        2.28 -     2.86: 5144
        2.86 -     3.44: 5574
        3.44 -     4.02: 7456
        4.02 -     4.60: 10922
  Nonbonded interactions: 29395
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.705 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.707 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.792 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.797 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.807 1.850
  ... (remaining 29390 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.02, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.388, 83.244, 55.913, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.895, 71.531, 45.409, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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.


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

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

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  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.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 80
        1.23 -     1.43: 392
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.93e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.83e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.59e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.57e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.50e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.12 -   105.92: 93
      105.92 -   111.72: 2426
      111.72 -   117.51: 547
      117.51 -   123.31: 830
      123.31 -   129.11: 183
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.24    4.36 1.00e+00 1.00e+00 1.90e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.65    5.55 1.30e+00 5.92e-01 1.82e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.82    5.38 1.30e+00 5.92e-01 1.71e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.00    5.20 1.30e+00 5.92e-01 1.60e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.80    3.80 1.00e+00 1.00e+00 1.45e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 962
       17.99 -    35.98: 49
       35.98 -    53.98: 16
       53.98 -    71.97: 3
       71.97 -    89.96: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.44   20.56     0      5.00e+00 4.00e-02 1.69e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.36   15.64     0      5.00e+00 4.00e-02 9.79e+00
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.37    7.77     0      2.50e+00 1.60e-01 9.65e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.050: 80
       0.050 -    0.100: 51
       0.100 -    0.149: 38
       0.149 -    0.199: 6
       0.199 -    0.248: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.81e-01
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.39e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.073 2.00e-02 2.50e+03   3.58e-02 3.85e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.045 2.00e-02 2.50e+03   3.15e-02 2.97e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.079 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.045 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.059 2.00e-02 2.50e+03   2.56e-02 1.97e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 300
        2.28 -     2.86: 5095
        2.86 -     3.44: 5567
        3.44 -     4.02: 7412
        4.02 -     4.60: 10755
  Nonbonded interactions: 29129
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.702 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.803 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.809 1.730
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.813 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.830 1.850
  ... (remaining 29124 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: 1.08
  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.


  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      : 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=  2.648)
  Mean delta:    0.013 (Z=  0.661)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.30     4.30  1.00e+00  1.85e+01   4.3*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.58     4.02  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.086 (Z=  4.300)
  Mean delta:    1.796 (Z=  0.989)

                      ----------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   157.62    22.38  5.00e+00  2.00e+01   4.5*sigma

  Min. delta:    0.022
  Max. delta:   76.883
  Mean delta:   13.482

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.238
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.085
  Mean delta:    0.016

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


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

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

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

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

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

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

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

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (58.02, 53.907, 51.446, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.471
    Angle     :  1.661   8.086   4079  Z= 0.735
    Chirality :  0.082   0.238    176
    Planarity :  0.011   0.067    327
    Dihedral  : 12.439  80.060    769
    Min Nonbonded Distance : 1.700
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    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: -1.35 (0.67), residues: 137
    helix: -1.09 (0.45), residues: 92
    sheet: -2.61 (1.21), residues: 10
    loop :  1.01 (1.23), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.040   0.008   PHE A  67 
   TYR   0.070   0.015   TYR A  12 
   ARG   0.069   0.023   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.028   0.007   PHE A  67 
   TYR   0.060   0.016   TYR A  12 
   ARG   0.007   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: 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 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.45e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    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 138 " segid="A   "
       model="   0" pdb=" CE1 HIS A 138 " segid="A   "
    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=" CZ  ARG A  58 " segid="A   "
       model="   0" pdb=" NH2 ARG A  58 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.02e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.45 -   106.25: 124
      106.25 -   112.04: 2480
      112.04 -   117.83: 480
      117.83 -   123.62: 866
      123.62 -   129.41: 129
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.46    4.14 1.00e+00 1.00e+00 1.72e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.85    5.35 1.30e+00 5.92e-01 1.70e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CB  HIS A 138 " segid="A   "
        model="   0" pdb=" CG  HIS A 138 " segid="A   "
        model="   0" pdb=" CD2 HIS A 138 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.17    5.03 1.30e+00 5.92e-01 1.50e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 964
       17.99 -    35.99: 45
       35.99 -    53.98: 19
       53.98 -    71.97: 2
       71.97 -    89.96: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.28   29.72     0      5.00e+00 4.00e-02 3.53e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.48   15.52     0      5.00e+00 4.00e-02 9.63e+00
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.19    7.59     0      2.50e+00 1.60e-01 9.21e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 72
       0.047 -    0.093: 55
       0.093 -    0.139: 38
       0.139 -    0.185: 9
       0.185 -    0.231: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  THR A  83 " segid="A   "
            model="   0" pdb=" N   THR A  83 " segid="A   "
            model="   0" pdb=" C   THR A  83 " segid="A   "
            model="   0" pdb=" CB  THR A  83 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.19 2.00e-01 2.50e+01 9.23e-01
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.72e-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 " segid="A   "   -0.076 2.00e-02 2.50e+03   3.47e-02 3.61e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.073 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.032 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.059 2.00e-02 2.50e+03   3.19e-02 3.04e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 " segid="A   "   -0.059 2.00e-02 2.50e+03   2.61e-02 2.04e+01
        model="   0" pdb=" CG  TYR A  89 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 " segid="A   "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 " segid="A   "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.35: 579
        2.35 -     2.91: 5231
        2.91 -     3.47: 5448
        3.47 -     4.04: 7303
        4.04 -     4.60: 10636
  Nonbonded interactions: 29197
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.784 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.786 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.786 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.794 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.801 1.850
  ... (remaining 29192 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: ""

  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: ""
  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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.406 -0.032 1.10e-02 8.26e+03 8.21e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    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=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.85e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.26e+00
  bond model="   0" pdb=" CZ  ARG A  58 " segid="A   "
       model="   0" pdb=" NH2 ARG A  58 " segid="A   "
    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:
       99.78 -   105.69: 80
      105.69 -   111.60: 2419
      111.60 -   117.51: 565
      117.51 -   123.42: 849
      123.42 -   129.33: 166
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.99    4.61 1.00e+00 1.00e+00 2.13e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.68    3.92 1.00e+00 1.00e+00 1.53e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.12    5.08 1.30e+00 5.92e-01 1.53e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.33   -4.93 1.40e+00 5.10e-01 1.24e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.71    4.49 1.30e+00 5.92e-01 1.19e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.15: 944
       15.15 -    30.30: 56
       30.30 -    45.44: 24
       45.44 -    60.59: 7
       60.59 -    75.74: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.97   22.03     0      5.00e+00 4.00e-02 1.94e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.89   16.11     0      5.00e+00 4.00e-02 1.04e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.21   15.79     0      5.00e+00 4.00e-02 9.97e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 72
       0.047 -    0.094: 56
       0.094 -    0.140: 32
       0.140 -    0.187: 13
       0.187 -    0.234: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  SER A  90 " segid="A   "
            model="   0" pdb=" N   SER A  90 " segid="A   "
            model="   0" pdb=" C   SER A  90 " segid="A   "
            model="   0" pdb=" CB  SER A  90 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+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 " segid="A   "    0.083 2.00e-02 2.50e+03   3.70e-02 4.11e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.016 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.069 2.00e-02 2.50e+03   3.00e-02 2.70e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.024 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.059 2.00e-02 2.50e+03   2.75e-02 2.27e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.027 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 345
        2.30 -     2.88: 5201
        2.88 -     3.45: 5461
        3.45 -     4.03: 7309
        4.03 -     4.60: 10623
  Nonbonded interactions: 28939
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.730 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  49 " segid="A   "
            model="   0" pdb=" HZ1 LYS A 113 " segid="A   "
     model   vdw
     1.791 1.730
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  40 " segid="A   "
     model   vdw
     1.793 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.803 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.812 1.730
  ... (remaining 28934 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   0.96

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: ""
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}

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.22 seconds

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

  Time building chain proxies: 0.96, per 1000 atoms: 0.43
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (76.381, 55.514, 48.755, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.42e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.92e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.48e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.17e+00
  bond model="   0" pdb=" ND1 HIS A 135 " segid="A   "
       model="   0" pdb=" CE1 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.74e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.75 -   105.67: 75
      105.67 -   111.58: 2397
      111.58 -   117.50: 594
      117.50 -   123.41: 851
      123.41 -   129.33: 162
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.92    4.68 1.00e+00 1.00e+00 2.19e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.22    4.38 1.00e+00 1.00e+00 1.92e+01
  angle model="   0" pdb=" C   LYS A  85 " segid="A   "
        model="   0" pdb=" N   ILE A  86 " segid="A   "
        model="   0" pdb=" CA  ILE A  86 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.70  128.96   -7.26 1.80e+00 3.09e-01 1.62e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.53    4.67 1.30e+00 5.92e-01 1.29e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 946
       16.01 -    32.03: 64
       32.03 -    48.04: 15
       48.04 -    64.06: 5
       64.06 -    80.07: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 " segid="A   "
           model="   0" pdb=" C   ALA A 115 " segid="A   "
           model="   0" pdb=" N   ASP A 116 " segid="A   "
           model="   0" pdb=" CA  ASP A 116 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.09  -16.91     0      5.00e+00 4.00e-02 1.14e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.18   16.82     0      5.00e+00 4.00e-02 1.13e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 73
       0.047 -    0.093: 53
       0.093 -    0.140: 40
       0.140 -    0.187: 9
       0.187 -    0.233: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.41e-01
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.19e-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 " segid="A   "    0.050 2.00e-02 2.50e+03   3.54e-02 3.76e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.091 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.048 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.057 2.00e-02 2.50e+03   3.50e-02 3.68e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.047 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.050 2.00e-02 2.50e+03   3.11e-02 2.91e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.062 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 267
        2.27 -     2.85: 5014
        2.85 -     3.44: 5645
        3.44 -     4.02: 7437
        4.02 -     4.60: 10857
  Nonbonded interactions: 29220
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.689 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.725 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.774 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.819 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.821 1.730
  ... (remaining 29215 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: (56.778, 47.095, 46.813, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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}

============================== 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 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: 1.06
  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.

  Time building chain proxies: 0.76, per 1000 atoms: 0.34
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (58.62, 60.395, 51.822, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: ""
        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: 49
        1.23 -     1.42: 423
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.02e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.89e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.48e+00
  bond model="   0" pdb=" CB  THR A  82 " segid="A   "
       model="   0" pdb=" OG1 THR A  82 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.433  1.394  0.039 1.60e-02 3.91e+03 5.86e+00
  bond model="   0" pdb=" ND1 HIS A 135 " segid="A   "
       model="   0" pdb=" CE1 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.78e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.46 -   105.46: 77
      105.46 -   111.45: 2380
      111.45 -   117.44: 600
      117.44 -   123.43: 859
      123.43 -   129.43: 163
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.94    4.66 1.00e+00 1.00e+00 2.17e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.89    5.31 1.30e+00 5.92e-01 1.67e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.14    5.06 1.30e+00 5.92e-01 1.52e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.43   -5.03 1.40e+00 5.10e-01 1.29e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 963
       17.99 -    35.98: 48
       35.98 -    53.96: 17
       53.96 -    71.95: 2
       71.95 -    89.94: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      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 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.93   21.07     0      5.00e+00 4.00e-02 1.78e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.77   16.23     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 72
       0.046 -    0.092: 51
       0.092 -    0.139: 35
       0.139 -    0.185: 15
       0.185 -    0.231: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LEU A 119 " segid="A   "
            model="   0" pdb=" N   LEU A 119 " segid="A   "
            model="   0" pdb=" C   LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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=" CA  PRO A 117 " segid="A   "
            model="   0" pdb=" N   PRO A 117 " segid="A   "
            model="   0" pdb=" C   PRO A 117 " segid="A   "
            model="   0" pdb=" CB  PRO A 117 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.66e-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 " segid="A   "    0.121 2.00e-02 2.50e+03   5.59e-02 9.38e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.088 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.093 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.056 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.085 2.00e-02 2.50e+03   3.87e-02 4.50e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.081 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.022 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.070 2.00e-02 2.50e+03   3.76e-02 4.23e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.034 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.32: 391
        2.32 -     2.89: 5264
        2.89 -     3.46: 5589
        3.46 -     4.03: 7463
        4.03 -     4.60: 10927
  Nonbonded interactions: 29634
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.745 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.756 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.769 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.782 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.787 1.730
  ... (remaining 29629 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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.15e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.09e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.76e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.72e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.14e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.30 -   105.32: 62
      105.32 -   111.34: 2367
      111.34 -   117.36: 629
      117.36 -   123.38: 851
      123.38 -   129.40: 170
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.14    4.46 1.00e+00 1.00e+00 1.99e+01
  angle model="   0" pdb=" NH1 ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
        model="   0" pdb=" NH2 ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     119.30  113.65    5.65 1.30e+00 5.92e-01 1.89e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.37    4.83 1.30e+00 5.92e-01 1.38e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.53    4.67 1.30e+00 5.92e-01 1.29e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 950
       16.49 -    32.97: 59
       32.97 -    49.46: 11
       49.46 -    65.94: 8
       65.94 -    82.43: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 135 " segid="A   "
           model="   0" pdb=" C   HIS A 135 " segid="A   "
           model="   0" pdb=" N   HIS A 136 " segid="A   "
           model="   0" pdb=" CA  HIS A 136 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.37   23.63     0      5.00e+00 4.00e-02 2.23e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      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  HIS A 137 " segid="A   "
           model="   0" pdb=" C   HIS A 137 " segid="A   "
           model="   0" pdb=" N   HIS A 138 " segid="A   "
           model="   0" pdb=" CA  HIS A 138 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.74   21.26     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 72
       0.057 -    0.114: 69
       0.114 -    0.170: 30
       0.170 -    0.227: 3
       0.227 -    0.284: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 135 " segid="A   "
            model="   0" pdb=" N   HIS A 135 " segid="A   "
            model="   0" pdb=" C   HIS A 135 " segid="A   "
            model="   0" pdb=" CB  HIS A 135 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    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=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    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  91 " segid="A   "   -0.121 2.00e-02 2.50e+03   4.73e-02 6.71e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.067 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.010 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.080 2.00e-02 2.50e+03   3.72e-02 4.16e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.079 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.036 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.068 2.00e-02 2.50e+03   3.17e-02 3.02e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 286
        2.28 -     2.86: 5115
        2.86 -     3.44: 5628
        3.44 -     4.02: 7365
        4.02 -     4.60: 10925
  Nonbonded interactions: 29319
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.699 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.792 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.795 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.802 1.850
  ... (remaining 29314 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.

  Time building chain proxies: 0.89, per 1000 atoms: 0.40
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.51, 58.313, 58.195, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.89 seconds

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


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

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (61.845, 73.8, 53.607, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 81
        1.23 -     1.43: 391
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.82e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.57e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.49e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.46e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.42e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.23 -   106.78: 178
      106.78 -   112.33: 2478
      112.33 -   117.89: 437
      117.89 -   123.44: 824
      123.44 -   128.99: 162
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.89    4.71 1.00e+00 1.00e+00 2.22e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      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  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.69    4.51 1.30e+00 5.92e-01 1.20e+01
  angle model="   0" pdb=" CA  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  115.99   -3.39 1.00e+00 1.00e+00 1.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 953
       16.01 -    32.03: 65
       32.03 -    48.04: 10
       48.04 -    64.05: 2
       64.05 -    80.07: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.76   17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.47    7.87     0      2.50e+00 1.60e-01 9.90e+00
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.34   15.66     0      5.00e+00 4.00e-02 9.81e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 75
       0.049 -    0.098: 59
       0.098 -    0.147: 31
       0.147 -    0.195: 10
       0.195 -    0.244: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality model="   0" pdb=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.71e-01
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.65e-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 " segid="A   "   -0.061 2.00e-02 2.50e+03   3.62e-02 3.93e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.048 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.079 2.00e-02 2.50e+03   3.58e-02 3.85e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.075 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.053 2.00e-02 2.50e+03   2.93e-02 2.57e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 326
        2.30 -     2.87: 5164
        2.87 -     3.45: 5453
        3.45 -     4.02: 7335
        4.02 -     4.60: 10740
  Nonbonded interactions: 29018
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.722 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.812 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.817 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.827 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  49 " segid="A   "
            model="   0" pdb=" HZ1 LYS A 113 " segid="A   "
     model   vdw
     1.838 1.730
  ... (remaining 29013 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.70, per 1000 atoms: 0.32
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.676, 48.601, 49.789, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A 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: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.53e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.00e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.65e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.36e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.36e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.95 -   106.94: 188
      106.94 -   112.93: 2543
      112.93 -   118.93: 453
      118.93 -   124.92: 833
      124.92 -   130.91: 62
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.91   -6.51 1.40e+00 5.10e-01 2.16e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.97    4.63 1.00e+00 1.00e+00 2.14e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 118 " segid="A   "
        model="   0" pdb=" C   ASP A 118 " segid="A   "
        model="   0" pdb=" N   LEU A 119 " segid="A   "
      ideal   model   delta    sigma   weight residual
     116.20  124.19   -7.99 2.00e+00 2.50e-01 1.60e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.59    4.61 1.30e+00 5.92e-01 1.26e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 945
       16.01 -    32.03: 60
       32.03 -    48.04: 22
       48.04 -    64.05: 3
       64.05 -    80.07: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.83   18.17     0      5.00e+00 4.00e-02 1.32e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.15   15.85     0      5.00e+00 4.00e-02 1.00e+01
  dihedral model="   0" pdb=" CA  LEU A 119 " segid="A   "
           model="   0" pdb=" C   LEU A 119 " segid="A   "
           model="   0" pdb=" N   GLU A 120 " segid="A   "
           model="   0" pdb=" CA  GLU A 120 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.20   15.80     0      5.00e+00 4.00e-02 9.98e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.050: 80
       0.050 -    0.099: 56
       0.099 -    0.148: 27
       0.148 -    0.197: 10
       0.197 -    0.246: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality model="   0" pdb=" CA  LEU A 119 " segid="A   "
            model="   0" pdb=" N   LEU A 119 " segid="A   "
            model="   0" pdb=" C   LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+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 " segid="A   "    0.070 2.00e-02 2.50e+03   3.28e-02 3.23e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.066 2.00e-02 2.50e+03   2.92e-02 2.55e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.023 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.064 2.00e-02 2.50e+03   2.83e-02 2.40e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.024 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 340
        2.30 -     2.87: 5197
        2.87 -     3.45: 5587
        3.45 -     4.02: 7457
        4.02 -     4.60: 10819
  Nonbonded interactions: 29400
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.721 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.803 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.830 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.832 1.850
  nonbonded model="   0" pdb=" O   ILE A  30 " segid="A   "
            model="   0" pdb=" HG1 THR A  34 " segid="A   "
     model   vdw
     1.839 1.850
  ... (remaining 29395 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 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.

  Time building chain proxies: 1.23, per 1000 atoms: 0.55
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.277, 60.307, 52.666, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

  Time building geometry restraints manager: 1.22 seconds

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  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.

  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 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.86e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.14e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.12e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.02e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.87e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.84 -   106.51: 151
      106.51 -   112.19: 2481
      112.19 -   117.87: 454
      117.87 -   123.55: 844
      123.55 -   129.23: 149
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
        model="   0" pdb=" NH2 ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     119.20  123.71   -4.51 9.00e-01 1.23e+00 2.52e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.85    4.75 1.00e+00 1.00e+00 2.26e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" CG  LYS A  19 " segid="A   "
        model="   0" pdb=" CD  LYS A  19 " segid="A   "
        model="   0" pdb=" CE  LYS A  19 " segid="A   "
      ideal   model   delta    sigma   weight residual
     111.30  103.05    8.25 2.30e+00 1.89e-01 1.29e+01
  angle model="   0" pdb=" NH1 ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
        model="   0" pdb=" NH2 ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     119.30  114.65    4.65 1.30e+00 5.92e-01 1.28e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 971
       16.07 -    32.14: 42
       32.14 -    48.21: 12
       48.21 -    64.28: 5
       64.28 -    80.35: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.00   19.00     0      5.00e+00 4.00e-02 1.44e+01
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.21   15.79     0      5.00e+00 4.00e-02 9.98e+00
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.59   15.41     0      5.00e+00 4.00e-02 9.50e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 79
       0.052 -    0.103: 58
       0.103 -    0.154: 32
       0.154 -    0.205: 5
       0.205 -    0.257: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  90 " segid="A   "
            model="   0" pdb=" N   SER A  90 " segid="A   "
            model="   0" pdb=" C   SER A  90 " segid="A   "
            model="   0" pdb=" CB  SER A  90 " segid="A   "
    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  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.13e-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 " segid="A   "    0.064 2.00e-02 2.50e+03   3.35e-02 3.37e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.031 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.072 2.00e-02 2.50e+03   3.32e-02 3.30e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.013 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.068 2.00e-02 2.50e+03   2.99e-02 2.68e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.026 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 373
        2.32 -     2.89: 5244
        2.89 -     3.46: 5519
        3.46 -     4.03: 7392
        4.03 -     4.60: 10868
  Nonbonded interactions: 29396
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.749 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.754 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.764 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.779 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.829 1.850
  ... (remaining 29391 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: 98
        1.23 -     1.43: 374
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.73e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.44e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.30e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.65e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.399 -0.025 1.10e-02 8.26e+03 5.28e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.64 -   106.33: 136
      106.33 -   112.02: 2468
      112.02 -   117.71: 472
      117.71 -   123.41: 841
      123.41 -   129.10: 162
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.91    4.69 1.00e+00 1.00e+00 2.20e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.18    4.42 1.00e+00 1.00e+00 1.95e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.14    5.06 1.30e+00 5.92e-01 1.51e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.15    5.05 1.30e+00 5.92e-01 1.51e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.87: 948
       15.87 -    31.74: 58
       31.74 -    47.60: 22
       47.60 -    63.47: 3
       63.47 -    79.34: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 " segid="A   "
           model="   0" pdb=" C   ALA A 115 " segid="A   "
           model="   0" pdb=" N   ASP A 116 " segid="A   "
           model="   0" pdb=" CA  ASP A 116 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.92   21.08     0      5.00e+00 4.00e-02 1.78e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.93   21.07     0      5.00e+00 4.00e-02 1.78e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 90
       0.050 -    0.101: 43
       0.101 -    0.151: 36
       0.151 -    0.201: 5
       0.201 -    0.251: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    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  50 " segid="A   "   -0.040 2.00e-02 2.50e+03   4.99e-02 7.48e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.126 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.084 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.038 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03   3.28e-02 3.24e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.052 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A  43 " segid="A   "   -0.061 2.00e-02 2.50e+03   3.93e-02 3.09e+01
        model="   0" pdb=" CG  HIS A  43 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 " segid="A   "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 " segid="A   "   -0.046 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 273
        2.27 -     2.86: 5110
        2.86 -     3.44: 5618
        3.44 -     4.02: 7474
        4.02 -     4.60: 11103
  Nonbonded interactions: 29578
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.692 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.808 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.812 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.819 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  49 " segid="A   "
            model="   0" pdb=" HZ1 LYS A 113 " segid="A   "
     model   vdw
     1.828 1.730
  ... (remaining 29573 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: 38
        1.23 -     1.42: 434
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.23e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.01e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.42e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    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=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.97e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.70 -   105.64: 76
      105.64 -   111.58: 2404
      111.58 -   117.52: 587
      117.52 -   123.46: 848
      123.46 -   129.40: 164
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.74    4.86 1.00e+00 1.00e+00 2.36e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      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=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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 -    17.98: 965
       17.98 -    35.97: 53
       35.97 -    53.95: 12
       53.95 -    71.94: 0
       71.94 -    89.92: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.36   17.64     0      5.00e+00 4.00e-02 1.25e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.74   15.26     0      5.00e+00 4.00e-02 9.32e+00
  dihedral model="   0" pdb=" N   HIS A 135 " segid="A   "
           model="   0" pdb=" CA  HIS A 135 " segid="A   "
           model="   0" pdb=" CB  HIS A 135 " segid="A   "
           model="   0" pdb=" CG  HIS A 135 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -112.47   52.47     3      1.50e+01 4.44e-03 9.12e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 74
       0.046 -    0.093: 53
       0.093 -    0.139: 35
       0.139 -    0.185: 11
       0.185 -    0.231: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.74e-01
  chirality model="   0" pdb=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.73e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.048 2.00e-02 2.50e+03   3.44e-02 3.54e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.088 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.046 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.075 2.00e-02 2.50e+03   3.42e-02 3.50e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.059 2.00e-02 2.50e+03   3.03e-02 2.75e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 312
        2.29 -     2.87: 5105
        2.87 -     3.45: 5491
        3.45 -     4.02: 7323
        4.02 -     4.60: 10583
  Nonbonded interactions: 28814
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.713 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.768 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.770 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.776 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.809 1.730
  ... (remaining 28809 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: ""
Symmetry information was not found, putting molecule in P1 box.

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

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

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'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: 1.08 seconds

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


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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 60
        1.23 -     1.42: 412
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.92e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.70e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.26e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.97e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.62e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.77 -   105.73: 87
      105.73 -   111.69: 2433
      111.69 -   117.65: 554
      117.65 -   123.61: 870
      123.61 -   129.57: 135
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.98    4.62 1.00e+00 1.00e+00 2.13e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.20    4.40 1.00e+00 1.00e+00 1.94e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.86    5.34 1.30e+00 5.92e-01 1.69e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.26    4.94 1.30e+00 5.92e-01 1.44e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.57   -5.17 1.40e+00 5.10e-01 1.36e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 968
       17.99 -    35.98: 46
       35.98 -    53.97: 14
       53.97 -    71.97: 3
       71.97 -    89.96: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.07   33.93     0      5.00e+00 4.00e-02 4.60e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.41   17.59     0      5.00e+00 4.00e-02 1.24e+01
  dihedral model="   0" pdb=" N   ARG A 129 " segid="A   "
           model="   0" pdb=" CA  ARG A 129 " segid="A   "
           model="   0" pdb=" CB  ARG A 129 " segid="A   "
           model="   0" pdb=" CG  ARG A 129 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.00  -57.00     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 73
       0.048 -    0.097: 54
       0.097 -    0.145: 38
       0.145 -    0.193: 7
       0.193 -    0.241: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+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 " segid="A   "   -0.053 2.00e-02 2.50e+03   3.59e-02 3.86e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.045 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03   3.30e-02 3.26e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.021 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "   -0.074 2.00e-02 2.50e+03   2.94e-02 2.60e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.019 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 288
        2.28 -     2.86: 5108
        2.86 -     3.44: 5513
        3.44 -     4.02: 7286
        4.02 -     4.60: 10817
  Nonbonded interactions: 29012
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.705 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.764 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.798 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.798 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.804 1.850
  ... (remaining 29007 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.71, per 1000 atoms: 0.32
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.823, 53.03, 49.288, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: ""
  Time building chain proxies: 1.24, per 1000 atoms: 0.56
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (61.651, 56.331, 53.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 0.80
  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.


  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: 1.11 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: 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.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 74
        1.23 -     1.43: 398
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.71e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.31e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.81e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.25e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.21e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.68 -   105.61: 75
      105.61 -   111.54: 2385
      111.54 -   117.47: 603
      117.47 -   123.40: 847
      123.40 -   129.32: 169
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.12    5.08 1.30e+00 5.92e-01 1.53e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.96    3.64 1.00e+00 1.00e+00 1.33e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.32   -4.92 1.40e+00 5.10e-01 1.24e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.75    4.45 1.30e+00 5.92e-01 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.40: 949
       15.40 -    30.80: 58
       30.80 -    46.20: 17
       46.20 -    61.60: 7
       61.60 -    77.00: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      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  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.26   14.74     0      5.00e+00 4.00e-02 8.69e+00
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.95    7.35     0      2.50e+00 1.60e-01 8.63e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 69
       0.047 -    0.093: 56
       0.093 -    0.139: 36
       0.139 -    0.185: 13
       0.185 -    0.231: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    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=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.53e-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 " segid="A   "   -0.044 2.00e-02 2.50e+03   4.76e-02 6.80e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.121 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.077 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.025 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.050 2.00e-02 2.50e+03   3.57e-02 3.83e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.091 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.049 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.066 2.00e-02 2.50e+03   3.34e-02 3.34e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 280
        2.28 -     2.86: 5095
        2.86 -     3.44: 5549
        3.44 -     4.02: 7352
        4.02 -     4.60: 10829
  Nonbonded interactions: 29105
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.699 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.739 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.767 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.792 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  49 " segid="A   "
            model="   0" pdb=" HZ1 LYS A 113 " segid="A   "
     model   vdw
     1.824 1.730
  ... (remaining 29100 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 73
        1.23 -     1.43: 399
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.409 -0.035 1.10e-02 8.26e+03 1.01e+01
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.40e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.19e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.41e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.38e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.26 -   105.33: 61
      105.33 -   111.40: 2385
      111.40 -   117.47: 612
      117.47 -   123.54: 873
      123.54 -   129.61: 148
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.01    4.59 1.00e+00 1.00e+00 2.11e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.61   -5.21 1.40e+00 5.10e-01 1.38e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.66    4.54 1.30e+00 5.92e-01 1.22e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      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 -    16.41: 951
       16.41 -    32.82: 61
       32.82 -    49.23: 14
       49.23 -    65.64: 4
       65.64 -    82.05: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.71   19.29     0      5.00e+00 4.00e-02 1.49e+01
  dihedral model="   0" pdb=" CA  MET A   1 " segid="A   "
           model="   0" pdb=" C   MET A   1 " segid="A   "
           model="   0" pdb=" N   LEU A   2 " segid="A   "
           model="   0" pdb=" CA  LEU A   2 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.33   17.67     0      5.00e+00 4.00e-02 1.25e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.32   16.68     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 69
       0.050 -    0.100: 60
       0.100 -    0.150: 35
       0.150 -    0.199: 10
       0.199 -    0.249: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.55e-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 " segid="A   "    0.115 2.00e-02 2.50e+03   5.55e-02 9.24e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.094 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.088 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.065 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.082 2.00e-02 2.50e+03   3.59e-02 3.86e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.028 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.069 2.00e-02 2.50e+03   3.38e-02 3.44e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 328
        2.30 -     2.87: 5175
        2.87 -     3.45: 5594
        3.45 -     4.02: 7392
        4.02 -     4.60: 10938
  Nonbonded interactions: 29427
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.725 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.753 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.800 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.811 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.821 1.730
  ... (remaining 29422 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   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 -     1.04: 1106
        1.04 -     1.23: 82
        1.23 -     1.43: 390
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.41e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.22e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.96e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.96e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.53e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.24 -   106.89: 184
      106.89 -   112.55: 2505
      112.55 -   118.20: 433
      118.20 -   123.86: 821
      123.86 -   129.51: 136
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.81    4.79 1.00e+00 1.00e+00 2.29e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.98    4.62 1.00e+00 1.00e+00 2.13e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.60    4.00 1.00e+00 1.00e+00 1.60e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.06    5.14 1.30e+00 5.92e-01 1.56e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.34    4.86 1.30e+00 5.92e-01 1.40e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.59: 938
       15.59 -    31.18: 66
       31.18 -    46.77: 23
       46.77 -    62.36: 4
       62.36 -    77.95: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      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  VAL A 112 " segid="A   "
           model="   0" pdb=" C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.98   16.02     0      5.00e+00 4.00e-02 1.03e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.01   15.99     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 69
       0.047 -    0.094: 57
       0.094 -    0.140: 37
       0.140 -    0.187: 12
       0.187 -    0.233: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.36e-01
  chirality model="   0" pdb=" CA  ILE A  86 " segid="A   "
            model="   0" pdb=" N   ILE A  86 " segid="A   "
            model="   0" pdb=" C   ILE A  86 " segid="A   "
            model="   0" pdb=" CB  ILE A  86 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.59e-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 " segid="A   "    0.112 2.00e-02 2.50e+03   5.60e-02 9.42e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.109 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.077 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.070 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.050 2.00e-02 2.50e+03   3.51e-02 3.70e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.090 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.046 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.060 2.00e-02 2.50e+03   3.15e-02 2.97e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 325
        2.29 -     2.87: 5189
        2.87 -     3.45: 5568
        3.45 -     4.02: 7460
        4.02 -     4.60: 10779
  Nonbonded interactions: 29321
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.715 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.765 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.808 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.817 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.827 1.850
  ... (remaining 29316 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}
Symmetry information was not found, putting molecule in P1 box.

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

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.03, 51.608, 55.456, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.09
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.22 seconds

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

  Time building chain proxies: 0.77, per 1000 atoms: 0.35
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (67.234, 62.305, 59.213, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.10
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.24 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   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: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 66
        1.23 -     1.42: 406
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.10e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.86e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.85e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.70e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.30e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.07 -   106.26: 124
      106.26 -   112.45: 2543
      112.45 -   118.63: 490
      118.63 -   124.82: 855
      124.82 -   131.00: 67
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  131.00   -6.60 1.40e+00 5.10e-01 2.22e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.21    4.39 1.00e+00 1.00e+00 1.93e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.95    3.65 1.00e+00 1.00e+00 1.33e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.56    4.64 1.30e+00 5.92e-01 1.27e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.55: 950
       15.55 -    31.10: 64
       31.10 -    46.64: 13
       46.64 -    62.19: 3
       62.19 -    77.74: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.56   20.44     0      5.00e+00 4.00e-02 1.67e+01
  dihedral model="   0" pdb=" CA  VAL A 112 " segid="A   "
           model="   0" pdb=" C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.81   18.19     0      5.00e+00 4.00e-02 1.32e+01
  dihedral model="   0" pdb=" CA  GLY A  87 " segid="A   "
           model="   0" pdb=" C   GLY A  87 " segid="A   "
           model="   0" pdb=" N   ASP A  88 " segid="A   "
           model="   0" pdb=" CA  ASP A  88 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.96  -18.04     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 71
       0.046 -    0.093: 51
       0.093 -    0.139: 39
       0.139 -    0.185: 13
       0.185 -    0.231: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.63e-01
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.11e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.072 2.00e-02 2.50e+03   3.27e-02 3.20e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.069 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.047 2.00e-02 2.50e+03   3.12e-02 2.91e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.076 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.014 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane m
  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.

odel="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.060 2.00e-02 2.50e+03   3.04e-02 2.78e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 334
        2.30 -     2.87: 5222
        2.87 -     3.45: 5561
        3.45 -     4.02: 7359
        4.02 -     4.60: 10842
  Nonbonded interactions: 29318
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.740 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.765 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.792 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.795 1.850
  ... (remaining 29313 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: ""
        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: 62
        1.23 -     1.42: 410
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.75e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.56e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.01e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.97e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.83e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.95 -   106.62: 158
      106.62 -   112.30: 2489
      112.30 -   117.98: 441
      117.98 -   123.66: 859
      123.66 -   129.34: 132
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.21    4.39 1.00e+00 1.00e+00 1.93e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.88    5.32 1.30e+00 5.92e-01 1.67e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.97    3.63 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.34   -4.94 1.40e+00 5.10e-01 1.24e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 949
       16.01 -    32.02: 50
       32.02 -    48.03: 24
       48.03 -    64.03: 6
       64.03 -    80.04: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 " segid="A   "
           model="   0" pdb=" C   ALA A 115 " segid="A   "
           model="   0" pdb=" N   ASP A 116 " segid="A   "
           model="   0" pdb=" CA  ASP A 116 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.45  -17.55     0      5.00e+00 4.00e-02 1.23e+01
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      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  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.12   15.88     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.048: 73
       0.048 -    0.095: 51
       0.095 -    0.141: 35
       0.141 -    0.188: 15
       0.188 -    0.235: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.85e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.65e-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 " segid="A   "    0.110 2.00e-02 2.50e+03   4.59e-02 6.31e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.090 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.013 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.065 2.00e-02 2.50e+03   3.13e-02 2.94e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.013 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane   Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 66
        1.23 -     1.43: 406
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.80e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.51e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.97e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.76e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.78e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.64 -   105.60: 80
      105.60 -   111.55: 2401
      111.55 -   117.51: 589
      117.51 -   123.47: 851
      123.47 -   129.43: 158
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.59    4.01 1.00e+00 1.00e+00 1.61e+01
  angle model="   0" pdb=" CA  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.35   -3.75 1.00e+00 1.00e+00 1.40e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.43   -5.03 1.40e+00 5.10e-01 1.29e+01
  angle model="   0" pdb=" CB  HIS A 138 " segid="A   "
        model="   0" pdb=" CG  HIS A 138 " segid="A   "
        model="   0" pdb=" CD2 HIS A 138 " segid="A   "
      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=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.72    4.48 1.30e+00 5.92e-01 1.19e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 967
       17.78 -    35.57: 44
       35.57 -    53.35: 15
       53.35 -    71.14: 3
       71.14 -    88.92: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.73   19.27     0      5.00e+00 4.00e-02 1.48e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.43   16.57     0      5.00e+00 4.00e-02 1.10e+01
  dihedral model="   0" pdb=" CB  GLU A 123 " segid="A   "
           model="   0" pdb=" Cmodel="   0" pdb=" CB  HIS A  43 " segid="A   "    0.048 2.00e-02 2.50e+03   2.97e-02 1.77e+01
        model="   0" pdb=" CG  HIS A  43 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 " segid="A   "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 " segid="A   "    0.025 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 316
        2.29 -     2.87: 5134
        2.87 -     3.45: 5517
        3.45 -     4.02: 7379
        4.02 -     4.60: 10665
  Nonbonded interactions: 29011
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.714 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.754 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.795 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.815 1.730
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  40 " segid="A   "
     model   vdw
     1.816 1.730
  ... (remaining 29006 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
G  GLU A 123 " segid="A   "
           model="   0" pdb=" CD  GLU A 123 " segid="A   "
           model="   0" pdb=" OE1 GLU A 123 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.92   88.92     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 62
       0.045 -    0.090: 57
       0.090 -    0.135: 41
       0.135 -    0.180: 13
       0.180 -    0.225: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality model="   0" pdb=" CA  PRO A 117 " segid="A   "
            model="   0" pdb=" N   PRO A 117 " segid="A   "
            model="   0" pdb=" C   PRO A 117 " segid="A   "
            model="   0" pdb=" CB  PRO A 117 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 8.17e-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 " segid="A   "    0.072 2.00e-02 2.50e+03   4.89e-02 7.19e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.126 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.047 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.071 2.00e-02 2.50e+03   3.59e-02 3.86e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.078 2.00e-02 2.50e+03   3.57e-02 3.83e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.076 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.033 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 304
        2.29 -     2.87: 5192
        2.87 -     3.44: 5582
        3.44 -     4.02: 7558
        4.02 -     4.60: 11113
  Nonbonded interactions: 29749
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.711 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.781 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.802 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.817 1.850
  ... (remaining 29744 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.646)
  Mean delta:    0.013 (Z=  0.661)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.60     4.00  1.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.147 (Z=  4.001)
  Mean delta:    1.792 (Z=  0.988)

                      ----------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   159.94    20.06  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.001
  Max. delta:   76.942
  Mean delta:   13.603

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.228
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.076
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.471
    Angle     :  1.660   8.147   4079  Z= 0.735
    Chirality :  0.082   0.228    176
    Planarity :  0.010   0.059    327
    Dihedral  : 12.421  80.025    769
    Min Nonbonded Distance : 1.705
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  1.61 %
      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: -1.18 (0.67), residues: 137
    helix: -1.07 (0.45), residues: 89
    sheet: -2.12 (1.24), residues: 10
    loop :  1.04 (1.19), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.036   0.008   PHE A  67 
   TYR   0.081   0.019   TYR A  91 
   ARG   0.066   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.025   0.007   PHE A  67 
   TYR   0.061   0.019   TYR A  68 
   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: 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.

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

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

  Time building chain proxies: 0.89, per 1000 atoms: 0.40
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.491, 49.812, 73.026, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   1.05

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: 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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.03e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.94e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.19e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.04e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.82e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.65 -   107.16: 399
      107.16 -   112.67: 2303
      112.67 -   118.18: 409
      118.18 -   123.69: 839
      123.69 -   129.20: 129
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.16    4.44 1.00e+00 1.00e+00 1.97e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.82    3.78 1.00e+00 1.00e+00 1.43e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.37    4.83 1.30e+00 5.92e-01 1.38e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.10    3.50 1.00e+00 1.00e+00 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 953
       16.01 -    32.02: 48
       32.02 -    48.02: 22
       48.02 -    64.03: 7
       64.03 -    80.04: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.78   16.22     0      5.00e+00 4.00e-02 1.05e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.05   15.95     0      5.00e+00 4.00e-02 1.02e+01
  dihedral model="   0" pdb=" N   HIS A 134 " segid="A   "
           model="   0" pdb=" CA  HIS A 134 " segid="A   "
           model="   0" pdb=" CB  HIS A 134 " segid="A   "
           model="   0" pdb=" CG  HIS A 134 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.69   58.69     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 73
       0.047 -    0.095: 53
       0.095 -    0.142: 35
       0.142 -    0.189: 14
       0.189 -    0.236: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.29e-01
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.51e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.054 2.00e-02 2.50e+03   3.74e-02 4.19e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.096 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.049 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.066 2.00e-02 2.50e+03   3.42e-02 3.50e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "   -0.080 2.00e-02 2.50e+03   3.11e-02 2.89e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.012 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 341
        2.30 -     2.88: 5167
        2.88 -     3.45: 5512
        3.45 -     4.03: 7303
        4.03 -     4.60: 10638
  Nonbonded interactions: 28961
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.728 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.775 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.788 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.809 1.730
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.811 1.850
  ... (remaining 28956 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: ""

  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: 1.08 seconds

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


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

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

  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=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.83e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.78e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.41e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.36e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.99e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.86 -   106.56: 170
      106.56 -   112.26: 2461
      112.26 -   117.97: 476
      117.97 -   123.67: 828
      123.67 -   129.37: 144
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.04    4.56 1.00e+00 1.00e+00 2.08e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.17    4.43 1.00e+00 1.00e+00 1.96e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.95    3.65 1.00e+00 1.00e+00 1.33e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.37   -4.97 1.40e+00 5.10e-01 1.26e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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 -    16.01: 948
       16.01 -    32.02: 60
       32.02 -    48.03: 19
       48.03 -    64.05: 3
       64.05 -    80.06: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A 122 " segid="A   "
           model="   0" pdb=" C   ILE A 122 " segid="A   "
           model="   0" pdb=" N   GLU A 123 " segid="A   "
           model="   0" pdb=" CA  GLU A 123 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.57   29.43     0      5.00e+00 4.00e-02 3.46e+01
  dihedral model="   0" pdb=" CA  HIS A 138 " segid="A   "
           model="   0" pdb=" C   HIS A 138 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.31   28.69     0      5.00e+00 4.00e-02 3.29e+01
  dihedral model="   0" pdb=" CA  ARG A 127 " segid="A   "
           model="   0" pdb=" C   ARG A 127 " segid="A   "
           model="   0" pdb=" N   MET A 128 " segid="A   "
           model="   0" pdb=" CA  MET A 128 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.49   24.51     0      5.00e+00 4.00e-02 2.40e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 68
       0.047 -    0.093: 59
       0.093 -    0.139: 36
       0.139 -    0.186: 12
       0.186 -    0.232: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.41e-01
  chirality model="   0" pdb=" CA  ILE A  86 " segid="A   "
            model="   0" pdb=" N   ILE A  86 " segid="A   "
            model="   0" pdb=" C   ILE A  86 " segid="A   "
            model="   0" pdb=" CB  ILE A  86 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.23e-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 " segid="A   "   -0.081 2.00e-02 2.50e+03   3.58e-02 3.84e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.074 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03   3.02e-02 2.74e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.042 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.045 2.00e-02 2.50e+03   2.91e-02 2.53e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.31: 352
        2.31 -     2.88: 5185
        2.88 -     3.45: 5326
        3.45 -     4.03: 6954
        4.03 -     4.60: 10378
  Nonbonded interactions: 28195
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.773 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.787 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.794 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.806 1.850
  ... (remaining 28190 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 53
        1.23 -     1.42: 419
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.42e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.11e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.53e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.39e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.24e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.55 -   105.52: 69
      105.52 -   111.48: 2375
      111.48 -   117.44: 619
      117.44 -   123.41: 850
      123.41 -   129.37: 166
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.19    4.41 1.00e+00 1.00e+00 1.95e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.63    3.97 1.00e+00 1.00e+00 1.58e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.49    4.71 1.30e+00 5.92e-01 1.31e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.37   -4.97 1.40e+00 5.10e-01 1.26e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.31   -4.91 1.40e+00 5.10e-01 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 950
       16.01 -    32.02: 58
       32.02 -    48.03: 19
       48.03 -    64.04: 3
       64.04 -    80.05: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.98   23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.34   21.66     0      5.00e+00 4.00e-02 1.88e+01
  dihedral model="   0" pdb=" CA  TYR A  81 " segid="A   "
           model="   0" pdb=" C   TYR A  81 " segid="A   "
           model="   0" pdb=" N   THR A  82 " segid="A   "
           model="   0" pdb=" CA  THR A  82 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.47   16.53     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 68
       0.047 -    0.094: 57
       0.094 -    0.140: 37
       0.140 -    0.187: 12
       0.187 -    0.234: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality model="   0" pdb=" CA  THR A  83 " segid="A   "
            model="   0" pdb=" N   THR A  83 " segid="A   "
            model="   0" pdb=" C   THR A  83 " segid="A   "
            model="   0" pdb=" CB  THR A  83 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.93e-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 " segid="A   "   -0.050 2.00e-02 2.50e+03   3.54e-02 3.76e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.091 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.046 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.072 2.00e-02 2.50e+03   3.30e-02 3.27e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.068 2.00e-02 2.50e+03   3.12e-02 2.92e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.030 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 364
        2.31 -     2.88: 5244
        2.88 -     3.45: 5577
        3.45 -     4.03: 7376
        4.03 -     4.60: 10813
  Nonbonded interactions: 29374
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.733 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.743 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.787 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.795 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.818 1.850
  ... (remaining 29369 not shown)

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

  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: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (86.83, 46.557, 47.049, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: (64.131, 58.572, 46.992, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

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

  Time building geometry restraints manager: 1.20 seconds

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

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (40.721, 56.429, 68.428, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 51
        1.23 -     1.42: 421
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.71e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.96e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.84e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.97e+00
  bond model="   0" pdb=" ND1 HIS A 137 " segid="A   "
       model="   0" pdb=" CE1 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.70e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.82 -   105.71: 78
      105.71 -   111.61: 2406
      111.61 -   117.50: 579
      117.50 -   123.39: 848
      123.39 -   129.28: 168
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.93    4.67 1.00e+00 1.00e+00 2.19e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.33    4.27 1.00e+00 1.00e+00 1.82e+01
  angle model="   0" pdb=" CA  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      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=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.12    5.08 1.30e+00 5.92e-01 1.53e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.61    4.59 1.30e+00 5.92e-01 1.25e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.85: 949
       15.85 -    31.70: 59
       31.70 -    47.55: 17
       47.55 -    63.40: 5
       63.40 -    79.25: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.42   22.58     0      5.00e+00 4.00e-02 2.04e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.62   15.38     0      5.00e+00 4.00e-02 9.46e+00
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.12    7.52     0      2.50e+00 1.60e-01 9.06e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 77
       0.048 -    0.097: 55
       0.097 -    0.145: 33
       0.145 -    0.193: 10
       0.193 -    0.241: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.63e-01
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.99e-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 " segid="A   "    0.036 2.00e-02 2.50e+03   4.73e-02 6.71e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.122 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.076 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.035 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.045 2.00e-02 2.50e+03   3.00e-02 2.70e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane m        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

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

odel="   0" pdb=" CB  HIS A  43 " segid="A   "    0.046 2.00e-02 2.50e+03   3.41e-02 2.32e+01
        model="   0" pdb=" CG  HIS A  43 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 " segid="A   "   -0.061 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 " segid="A   "    0.051 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 286
        2.28 -     2.86: 5101
        2.86 -     3.44: 5524
        3.44 -     4.02: 7271
        4.02 -     4.60: 10866
  Nonbonded interactions: 29048
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.703 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.741 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.768 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.783 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, 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: 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=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.99e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.95e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.90e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.13e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.11e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.74 -   105.70: 84
      105.70 -   111.66: 2419
      111.66 -   117.62: 571
      117.62 -   123.58: 851
      123.58 -   129.54: 154
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.99    4.61 1.00e+00 1.00e+00 2.12e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.21    4.39 1.00e+00 1.00e+00 1.92e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.54   -5.14 1.40e+00 5.10e-01 1.35e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" N   ASP A  36 " segid="A   "
        model="   0" pdb=" CA  ASP A  36 " segid="A   "
        model="   0" pdb=" CB  ASP A  36 " segid="A   "
      ideal   model   delta    sigma   weight residual
     110.50  104.89    5.61 1.70e+00 3.46e-01 1.09e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 964
       17.60 -    35.21: 50
       35.21 -    52.81: 12
       52.81 -    70.42: 5
       70.42 -    88.02: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A 121 " segid="A   "
           model="   0" pdb=" C   GLY A 121 " segid="A   "
           model="   0" pdb=" N   ILE A 122 " segid="A   "
           model="   0" pdb=" CA  ILE A 122 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.71   26.29     0      5.00e+00 4.00e-02 2.77e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.40   19.60     0      5.00e+00 4.00e-02 1.54e+01
  dihedral model="   0" pdb=" CA  ASP A 118 " segid="A   "
           model="   0" pdb=" C   ASP A 118 " segid="A   "
           model="   0" pdb=" N   LEU A 119 " segid="A   "
           model="   0" pdb=" CA  LEU A 119 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.23   16.77     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 71
       0.047 -    0.094: 51
       0.094 -    0.141: 36
       0.141 -    0.188: 14
       0.188 -    0.235: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A 118 " segid="A   "
            model="   0" pdb=" N   ASP A 118 " segid="A   "
            model="   0" pdb=" C   ASP A 118 " segid="A   "
            model="   0" pdb=" CB  ASP A 118 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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=" CA  PRO A 117 " segid="A   "
            model="   0" pdb=" N   PRO A 117 " segid="A   "
            model="   0" pdb=" C   PRO A 117 " segid="A   "
            model="   0" pdb=" CB  PRO A 117 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.065 2.00e-02 2.50e+03   3.40e-02 3.46e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.074 2.00e-02 2.50e+03   3.25e-02 3.17e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.051 2.00e-02 2.50e+03   2.73e-02 2.23e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 277
        2.28 -     2.86: 5119
        2.86 -     3.44: 5604
        3.44 -     4.02: 7402
        4.02 -     4.60: 10803
  Nonbonded interactions: 29205
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.698 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.707 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.708 1.850
  nonbonded model="   0" pdb=" OD1 ASP A 118 " segid="A   "
            model="   0" pdb=" HZ2 LYS A 125 " segid="A   "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.772 1.850
  ... (remaining 29200 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.879, 71.468, 45.184, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 seconds

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

  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.776, 52.717, 50.115, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 51
        1.23 -     1.42: 421
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.54e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.70e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.57e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.52e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.97 -   105.98: 104
      105.98 -   111.99: 2494
      111.99 -   118.00: 502
      118.00 -   124.01: 862
      124.01 -   130.02: 117
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 " segid="A   "
        model="   0" pdb=" N   ILE A  86 " segid="A   "
        model="   0" pdb=" CA  ILE A  86 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.70  130.02   -8.32 1.80e+00 3.09e-01 2.13e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.11    5.09 1.30e+00 5.92e-01 1.54e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      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=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.50    4.70 1.30e+00 5.92e-01 1.31e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 949
       16.01 -    32.03: 58
       32.03 -    48.04: 21
       48.04 -    64.05: 2
       64.05 -    80.06: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.29   22.71     0      5.00e+00 4.00e-02 2.06e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.66   18.34     0      5.00e+00 4.00e-02 1.34e+01
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      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:
       0.000 -    0.051: 78
       0.051 -    0.103: 65
       0.103 -    0.154: 28
       0.154 -    0.205: 4
       0.205 -    0.256: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.96e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 6.97e-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 " segid="A   "   -0.065 2.00e-02 2.50e+03   3.38e-02 3.42e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.022 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.046 2.00e-02 2.50e+03   3.16e-02 2.99e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.082 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.034 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.069 2.00e-02 2.50e+03   3.07e-02 2.83e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.027 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 273
        2.28 -     2.86: 5064
        2.86 -     3.44: 5472
        3.44 -     4.02: 7136
        4.02 -     4.60: 10582
  Nonbonded interactions: 28527
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.698 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.799 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.830 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.830 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.836 1.730
  ... (remaining 28522 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.84, per 1000 atoms: 0.38
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.962, 71.097, 45.217, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 0.80
  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.


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=  2.588)
  Mean delta:    0.013 (Z=  0.659)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.38     5.82  1.30e+00  2.00e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.20     4.40  1.00e+00  1.93e+01   4.4*sigma
   A  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:    0.002 (Z=  0.001)
  Max. delta:    9.364 (Z=  4.475)
  Mean delta:    1.900 (Z=  1.031)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   143.67    36.33  5.00e+00  5.28e+01   7.3*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   144.45    35.55  5.00e+00  5.06e+01   7.1*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   147.66    32.34  5.00e+00  4.18e+01   6.5*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   147.71    32.29  5.00e+00  4.17e+01   6.5*sigma
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   147.89    32.11  5.00e+00  4.12e+01   6.4*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   148.67    31.33  5.00e+00  3.93e+01   6.3*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00   151.46    28.54  5.00e+00  3.26e+01   5.7*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   157.52    22.48  5.00e+00  2.02e+01   4.5*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   159.86    20.14  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.023
  Max. delta:   78.525
  Mean delta:   13.851

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.308
  Mean delta:    0.086

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.078
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.728   9.364   4079  Z= 0.763
    Chirality :  0.086   0.308    176
    Planarity :  0.011   0.060    327
    Dihedral  : 12.591  89.969    769
    Min Nonbonded Distance : 1.731
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  :  8.76 %
      Favored  : 84.67 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  1.61 %
      Favored  : 96.77 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 4.58 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.21 (0.68), residues: 137
    helix: -1.42 (0.52), residues: 70
    sheet: -3.04 (0.95), residues: 10
    loop : -0.96 (0.95), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A  43 
   PHE   0.023   0.007   PHE A  67 
   TYR   0.089   0.018   TYR A  12 
   ARG   0.068   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A  43 
   PHE   0.020   0.005   PHE A  67 
   TYR   0.074   0.020   TYR A  12 
   ARG   0.005   0.001   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.42e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.77e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.84e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.49e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.30 -   106.09: 123
      106.09 -   111.89: 2445
      111.89 -   117.68: 513
      117.68 -   123.47: 832
      123.47 -   129.27: 166
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.50    5.10 1.00e+00 1.00e+00 2.60e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.90    4.70 1.00e+00 1.00e+00 2.21e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.89    5.31 1.30e+00 5.92e-01 1.67e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.09    3.51 1.00e+00 1.00e+00 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 954
       16.01 -    32.02: 61
       32.02 -    48.03: 13
       48.03 -    64.04: 2
       64.04 -    80.05: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A 122 " segid="A   "
           model="   0" pdb=" C   ILE A 122 " segid="A   "
           model="   0" pdb=" N   GLU A 123 " segid="A   "
           model="   0" pdb=" CA  GLU A 123 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.61   45.39     0      5.00e+00 4.00e-02 8.24e+01
  dihedral model="   0" pdb=" C   ILE A 122 " segid="A   "
           model="   0" pdb=" N   ILE A 122 " segid="A   "
           model="   0" pdb=" CA  ILE A 122 " segid="A   "
           model="   0" pdb=" CB  ILE A 122 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.09   14.09     0      2.50e+00 1.60e-01 3.18e+01
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.98   26.02     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.062: 81
       0.062 -    0.123: 64
       0.123 -    0.184: 28
       0.184 -    0.245: 1
       0.245 -    0.305: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A 122 " segid="A   "
            model="   0" pdb=" N   ILE A 122 " segid="A   "
            model="   0" pdb=" C   ILE A 122 " segid="A   "
            model="   0" pdb=" CB  ILE A 122 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.13    0.31 2.00e-01 2.50e+01 2.33e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    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  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.049 2.00e-02 2.50e+03   3.50e-02 3.67e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.090 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.046 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.065 2.00e-02 2.50e+03   3.45e-02 3.58e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.044 2.00e-02 2.50e+03   2.68e-02 2.15e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 341
        2.30 -     2.88: 5180
        2.88 -     3.45: 5425
        3.45 -     4.03: 7107
        4.03 -     4.60: 10483
  Nonbonded interactions: 28536
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.728 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.733 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.775 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.787 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.802 1.730
  ... (remaining 28531 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=  2.742)
  Mean delta:    0.013 (Z=  0.653)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   132.06    -7.66  1.40e+00  3.00e+01   5.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.20     4.40  1.00e+00  1.94e+01   4.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.35     4.25  1.00e+00  1.80e+01   4.2*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.85     5.35  1.30e+00  1.70e+01   4.1*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.91     5.29  1.30e+00  1.66e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.250 (Z=  5.474)
  Mean delta:    1.821 (Z=  1.010)

                      ----------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   150.19    29.81  5.00e+00  3.55e+01   6.0*sigma

  Min. delta:    0.043
  Max. delta:   79.028
  Mean delta:   12.559

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.286
  Mean delta:    0.085

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.048       0.096       45.76   4.8*sigma

  Min. delta:    0.000
  Max. delta:    0.073
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.465
    Angle     :  1.680   8.250   4079  Z= 0.748
    Chirality :  0.085   0.286    176
    Planarity :  0.010   0.055    327
    Dihedral  : 11.899  81.986    769
    Min Nonbonded Distance : 1.719
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    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: -0.72 (0.71), residues: 137
    helix: -1.06 (0.46), residues: 88
    sheet: -0.94 (1.81), residues: 10
    loop :  1.81 (1.22), residues: 39
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.005   HIS A  43 
   PHE   0.027   0.008   PHE A  45 
   TYR   0.125   0.018   TYR A  50 
   ARG   0.061   0.015   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.005   HIS A  43 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.096   0.017   TYR A  50 
   ARG   0.006   0.002   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   6.57 %
                favored =  84.67 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     1
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.73
  MolProbity score      =   1.48

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0090
  RMS(angles)           =   1.68
  MolProbity score      =   1.08

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: 1.08
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 55
        1.23 -     1.42: 417
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.53e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.01e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.73e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.39e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    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:
       99.77 -   105.69: 79
      105.69 -   111.62: 2416
      111.62 -   117.54: 568
      117.54 -   123.47: 861
      123.47 -   129.39: 155
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.86    4.74 1.00e+00 1.00e+00 2.24e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.34    4.26 1.00e+00 1.00e+00 1.82e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.11    5.09 1.30e+00 5.92e-01 1.54e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.39   -4.99 1.40e+00 5.10e-01 1.27e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.07    3.53 1.00e+00 1.00e+00 1.25e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.35: 951
       15.35 -    30.69: 61
       30.69 -    46.04: 16
       46.04 -    61.38: 3
       61.38 -    76.73: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.04   19.96     0      5.00e+00 4.00e-02 1.59e+01
  dihedral model="   0" pdb=" CA  VAL A 112 " segid="A   "
           model="   0" pdb=" C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.22   16.78     0      5.00e+00 4.00e-02 1.13e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.82   16.18     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 74
       0.049 -    0.098: 60
       0.098 -    0.148: 35
       0.148 -    0.197: 6
       0.197 -    0.246: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.37e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.65e-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 " segid="A   "    0.062 2.00e-02 2.50e+03   3.08e-02 2.85e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.023 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.070 2.00e-02 2.50e+03   3.01e-02 2.72e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.019 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.038 2.00e-02 2.50e+03   2.82e-02 2.38e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.040 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 298
        2.29 -     2.86: 5130
        2.86 -     3.44: 5539
        3.44 -     4.02: 7301
        4.02 -     4.60: 10853
  Nonbonded interactions: 29121
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.707 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.760 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.768 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.805 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.808 1.730
  ... (remaining 29116 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.642)
  Mean delta:    0.013 (Z=  0.661)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.07     4.53  1.00e+00  2.05e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.07     4.53  1.00e+00  2.05e+01   4.5*sigma

  Min. delta:    0.010 (Z=  0.002)
  Max. delta:    8.020 (Z=  4.533)
  Mean delta:    1.783 (Z=  0.986)

                      ----------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   154.40    25.60  5.00e+00  2.62e+01   5.1*sigma

  Min. delta:    0.015
  Max. delta:   80.524
  Mean delta:   12.669

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:    0.260
  Mean delta:    0.083

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.073
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.470
    Angle     :  1.655   8.020   4079  Z= 0.734
    Chirality :  0.083   0.260    176
    Planarity :  0.010   0.057    327
    Dihedral  : 11.708  89.955    769
    Min Nonbonded Distance : 1.712
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    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: -1.39 (0.66), residues: 137
    helix: -1.43 (0.43), residues: 87
    sheet: -1.65 (1.44), residues: 10
    loop :  1.17 (1.15), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.043   0.009   PHE A  67 
   TYR   0.095   0.017   TYR A  68 
   ARG   0.064   0.019   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.029   0.008   PHE A  67 
   TYR   0.073   0.016   TYR A  68 
   ARG   0.007   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=  0.001)
  Max. delta:    0.039 (Z=  2.683)
  Mean delta:    0.013 (Z=  0.660)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.21     4.39  1.00e+00  1.92e+01   4.4*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    8.034 (Z=  4.387)
  Mean delta:    1.764 (Z=  0.981)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   76.618
  Mean delta:   14.073

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.241
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.108
  Mean delta:    0.016

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


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

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

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

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

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

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.470
    Angle     :  1.641   8.034   4079  Z= 0.729
    Chirality :  0.082   0.241    176
    Planarity :  0.011   0.082    327
    Dihedral  : 12.278  76.618    769
    Min Nonbonded Distance : 1.704
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  3.23 %
      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: -1.12 (0.69), residues: 137
    helix: -1.25 (0.46), residues: 89
    sheet: -1.22 (1.68), residues: 10
    loop :  1.41 (1.16), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.061   0.011   PHE A  67 
   TYR   0.071   0.015   TYR A 111 
   ARG   0.089   0.024   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.041   0.010   PHE A  67 
   TYR   0.063   0.015   TYR A 111 
   ARG   0.006   0.002   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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


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

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

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   0.96

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.64
  MolProbity score      =   1.20

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: 80
        1.23 -     1.43: 392
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.40e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.81e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.20e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    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=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.75e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.18 -   106.78: 193
      106.78 -   112.38: 2454
      112.38 -   117.99: 448
      117.99 -   123.59: 842
      123.59 -   129.19: 142
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.09    4.51 1.00e+00 1.00e+00 2.04e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.31    4.89 1.30e+00 5.92e-01 1.42e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      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=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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 -    17.99: 968
       17.99 -    35.97: 49
       35.97 -    53.96: 13
       53.96 -    71.95: 0
       71.95 -    89.93: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.60   31.40     0      5.00e+00 4.00e-02 3.94e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.95   16.05     0      5.00e+00 4.00e-02 1.03e+01
  dihedral model="   0" pdb=" N   HIS A 137 " segid="A   "
           model="   0" pdb=" CA  HIS A 137 " segid="A   "
           model="   0" pdb=" CB  HIS A 137 " segid="A   "
           model="   0" pdb=" CG  HIS A 137 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.78  -53.22     3      1.50e+01 4.44e-03 9.19e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 73
       0.049 -    0.098: 61
       0.098 -    0.147: 32
       0.147 -    0.196: 8
       0.196 -    0.245: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality model="   0" pdb=" CA  HIS A 137 " segid="A   "
            model="   0" pdb=" N   HIS A 137 " segid="A   "
            model="   0" pdb=" C   HIS A 137 " segid="A   "
            model="   0" pdb=" CB  HIS A 137 " segid="A   "
    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=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    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 " segid="A   "   -0.088 2.00e-02 2.50e+03   3.56e-02 3.80e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.022 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.061 2.00e-02 2.50e+03   3.26e-02 3.19e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.046 2.00e-02 2.50e+03   3.14e-02 2.95e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.077 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.046 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 279
        2.28 -     2.86: 5105
        2.86 -     3.44: 5543
        3.44 -     4.02: 7419
        4.02 -     4.60: 10985
  Nonbonded interactions: 29331
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.696 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.737 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.779 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  40 " segid="A   "
     model   vdw
     1.793 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.803 1.730
  ... (remaining 29326 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 disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.76 seconds

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


  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: 1.05 seconds

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 75
        1.23 -     1.43: 397
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.25e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.19e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.10e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    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=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.71e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.82 -   106.56: 154
      106.56 -   112.29: 2501
      112.29 -   118.03: 445
      118.03 -   123.76: 851
      123.76 -   129.50: 128
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.87    4.73 1.00e+00 1.00e+00 2.24e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.84    5.36 1.30e+00 5.92e-01 1.70e+01
  angle model="   0" pdb=" CA  ASP A  88 " segid="A   "
        model="   0" pdb=" CB  ASP A  88 " segid="A   "
        model="   0" pdb=" CG  ASP A  88 " segid="A   "
      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  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.42    4.78 1.30e+00 5.92e-01 1.35e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 963
       16.91 -    33.81: 42
       33.81 -    50.72: 20
       50.72 -    67.62: 4
       67.62 -    84.53: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.22   15.78     0      5.00e+00 4.00e-02 9.96e+00
  dihedral model="   0" pdb=" CB  GLU A  32 " segid="A   "
           model="   0" pdb=" CG  GLU A  32 " segid="A   "
           model="   0" pdb=" CD  GLU A  32 " segid="A   "
           model="   0" pdb=" OE1 GLU A  32 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.53   84.53     1      3.00e+01 1.11e-03 9.65e+00
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.59   15.41     0      5.00e+00 4.00e-02 9.50e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 76
       0.046 -    0.091: 50
       0.091 -    0.137: 35
       0.137 -    0.182: 13
       0.182 -    0.227: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.13e-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 " segid="A   "   -0.075 2.00e-02 2.50e+03   3.38e-02 3.43e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.018 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.057 2.00e-02 2.50e+03   3.20e-02 3.08e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.044 2.00e-02 2.50e+03   3.07e-02 2.82e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.062 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.036 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 344
        2.31 -     2.88: 5218
        2.88 -     3.45: 5478
        3.45 -     4.03: 7343
        4.03 -     4.60: 10747
  Nonbonded interactions: 29130
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.733 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.775 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  40 " segid="A   "
     model   vdw
     1.782 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.785 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.806 1.730
  ... (remaining 29125 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: 42
        1.23 -     1.42: 430
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.42e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.87e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.48e+00
  bond model="   0" pdb=" ND1 HIS A 137 " segid="A   "
       model="   0" pdb=" CE1 HIS A 137 " segid="A   "
    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=" CB  THR A  82 " segid="A   "
       model="   0" pdb=" OG1 THR A  82 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.433  1.393  0.040 1.60e-02 3.91e+03 6.15e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.36 -   104.53: 34
      104.53 -   110.69: 2253
      110.69 -   116.86: 750
      116.86 -   123.03: 808
      123.03 -   129.20: 234
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.18    4.42 1.00e+00 1.00e+00 1.96e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.99    5.21 1.30e+00 5.92e-01 1.60e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.67    3.93 1.00e+00 1.00e+00 1.55e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      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 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.38    4.82 1.30e+00 5.92e-01 1.37e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 954
       15.99 -    31.97: 52
       31.97 -    47.96: 19
       47.96 -    63.95: 5
       63.95 -    79.94: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.48   28.52     0      5.00e+00 4.00e-02 3.25e+01
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.15   15.85     0      5.00e+00 4.00e-02 1.00e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.18   15.82     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 72
       0.048 -    0.096: 51
       0.096 -    0.143: 41
       0.143 -    0.191: 11
       0.191 -    0.239: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  46 " segid="A   "
            model="   0" pdb=" N   SER A  46 " segid="A   "
            model="   0" pdb=" C   SER A  46 " segid="A   "
            model="   0" pdb=" CB  SER A  46 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    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=" CA  PRO A 117 " segid="A   "
            model="   0" pdb=" N   PRO A 117 " segid="A   "
            model="   0" pdb=" C   PRO A 117 " segid="A   "
            model="   0" pdb=" CB  PRO A 117 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.81e-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 " segid="A   "   -0.147 2.00e-02 2.50e+03   6.68e-02 1.34e+02
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.118 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.097 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.066 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.052 2.00e-02 2.50e+03   3.60e-02 3.89e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.092 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.047 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.062 2.00e-02 2.50e+03   3.15e-02 2.97e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.25: 243
        2.25 -     2.84: 4856
        2.84 -     3.43: 5810
        3.43 -     4.01: 7557
        4.01 -     4.60: 11136
  Nonbonded interactions: 29602
  Sorted by model distance:
  nonbonded model="   0" pdb=" H1  MET A   1 " segid="A   "
            model="   0" pdb="HG22 VAL A 126 " segid="A   "
     model   vdw
     1.668 2.270
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.760 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.763 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.780 1.730
  ... (remaining 29597 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 53
        1.23 -     1.42: 419
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.86e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    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=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.67e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.33e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.32e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.81 -   105.95: 86
      105.95 -   112.09: 2525
      112.09 -   118.22: 514
      118.22 -   124.36: 860
      124.36 -   130.50: 94
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.81    4.79 1.00e+00 1.00e+00 2.30e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.50   -6.10 1.40e+00 5.10e-01 1.90e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.51    4.69 1.30e+00 5.92e-01 1.30e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 954
       16.00 -    32.01: 56
       32.01 -    48.01: 15
       48.01 -    64.02: 5
       64.02 -    80.02: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.86   15.14     0      5.00e+00 4.00e-02 9.17e+00
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.99    7.39     0      2.50e+00 1.60e-01 8.73e+00
  dihedral model="   0" pdb=" N   HIS A 135 " segid="A   "
           model="   0" pdb=" CA  HIS A 135 " segid="A   "
           model="   0" pdb=" CB  HIS A 135 " segid="A   "
           model="   0" pdb=" CG  HIS A 135 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.91   47.91     3      1.50e+01 4.44e-03 8.56e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 74
       0.047 -    0.093: 55
       0.093 -    0.140: 33
       0.140 -    0.186: 13
       0.186 -    0.233: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.31e-01
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    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  12 " segid="A   "   -0.072 2.00e-02 2.50e+03   3.28e-02 3.24e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.069 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.031 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.066 2.00e-02 2.50e+03   3.20e-02 3.06e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.030 2.00e-02 2.50e+03   2.61e-02 2.05e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.042 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 317
        2.29 -     2.87: 5149
        2.87 -     3.44: 5561
        3.44 -     4.02: 7377
        4.02 -     4.60: 10794
  Nonbonded interactions: 29198
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.712 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.713 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.800 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.830 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.838 1.850
  ... (remaining 29193 not shown)

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

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


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


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

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

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


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

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=  2.558)
  Mean delta:    0.013 (Z=  0.667)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.31     4.29  1.00e+00  1.84e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.85     5.35  1.30e+00  1.70e+01   4.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.735 (Z=  4.294)
  Mean delta:    1.746 (Z=  0.972)

                      ----------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   150.28    29.72  5.00e+00  3.53e+01   5.9*sigma

  Min. delta:    0.002
  Max. delta:   77.173
  Mean delta:   13.459

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.231
  Mean delta:    0.080

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.151
  Mean delta:    0.019

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.475
    Angle     :  1.636   7.735   4079  Z= 0.725
    Chirality :  0.080   0.231    176
    Planarity :  0.012   0.117    327
    Dihedral  : 12.261  89.963    769
    Min Nonbonded Distance : 1.784
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  4.03 %
      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: -1.01 (0.70), residues: 137
    helix: -1.01 (0.49), residues: 88
    sheet: -1.73 (1.38), residues: 10
    loop :  1.13 (1.18), residues: 39
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.002   HIS A  43 
   PHE   0.046   0.010   PHE A  67 
   TYR   0.076   0.017   TYR A  12 
   ARG   0.122   0.030   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.002   HIS A  43 
   PHE   0.032   0.010   PHE A  67 
   TYR   0.065   0.017   TYR A  12 
   ARG   0.009   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Time building chain proxies: 0.65, per 1000 atoms: 0.29
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.658, 63.846, 53.37, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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=  0.003)
  Max. delta:    0.038 (Z=  2.865)
  Mean delta:    0.013 (Z=  0.658)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.99     4.61  1.00e+00  2.13e+01   4.6*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.716 (Z=  4.614)
  Mean delta:    1.748 (Z=  0.966)

                      ----------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   157.97    22.03  5.00e+00  1.94e+01   4.4*sigma

  Min. delta:    0.029
  Max. delta:   75.741
  Mean delta:   13.587

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.234
  Mean delta:    0.084

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.100
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.635   7.716   4079  Z= 0.722
    Chirality :  0.084   0.234    176
    Planarity :  0.010   0.077    327
    Dihedral  : 11.847  75.741    769
    Min Nonbonded Distance : 1.730
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  1.61 %
      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: -1.32 (0.69), residues: 137
    helix: -1.39 (0.46), residues: 90
    sheet: -1.27 (1.48), residues: 10
    loop :  1.38 (1.23), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.041   0.008   PHE A  67 
   TYR   0.083   0.015   TYR A 111 
   ARG   0.084   0.020   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.028   0.007   PHE A  67 
   TYR   0.073   0.017   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 =   0.00 %
                favored =  94.89 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.64
  MolProbity score      =   0.85

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=  2.632)
  Mean delta:    0.013 (Z=  0.658)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.24     4.36  1.00e+00  1.90e+01   4.4*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.65     5.55  1.30e+00  1.82e+01   4.3*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.82     5.38  1.30e+00  1.71e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.183 (Z=  4.357)
  Mean delta:    1.788 (Z=  0.993)

                      ----------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   159.44    20.56  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.022
  Max. delta:   78.698
  Mean delta:   13.937

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.248
  Mean delta:    0.080

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.077
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.648   7.183   4079  Z= 0.735
    Chirality :  0.080   0.248    176
    Planarity :  0.010   0.059    327
    Dihedral  : 12.240  89.962    769
    Min Nonbonded Distance : 1.702
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    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: -1.34 (0.68), residues: 137
    helix: -1.06 (0.47), residues: 92
    sheet: -2.68 (1.15), residues: 10
    loop :  0.95 (1.26), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.049   0.009   PHE A  67 
   TYR   0.079   0.017   TYR A  68 
   ARG   0.067   0.016   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.033   0.009   PHE A  67 
   TYR   0.067   0.018   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      : 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=  2.745)
  Mean delta:    0.013 (Z=  0.654)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.06     4.54  1.00e+00  2.06e+01   4.5*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   116.92    -4.32  1.00e+00  1.86e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    8.046 (Z=  4.539)
  Mean delta:    1.772 (Z=  0.981)

                      ----------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   155.00    25.00  5.00e+00  2.50e+01   5.0*sigma

  Min. delta:    0.001
  Max. delta:   79.768
  Mean delta:   13.041

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.257
  Mean delta:    0.083

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.084
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.466
    Angle     :  1.643   8.046   4079  Z= 0.729
    Chirality :  0.083   0.257    176
    Planarity :  0.010   0.064    327
    Dihedral  : 11.531  79.768    769
    Min Nonbonded Distance : 1.705
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    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: -0.94 (0.67), residues: 137
    helix: -0.91 (0.47), residues: 90
    sheet: -2.23 (1.17), residues: 10
    loop :  1.34 (1.17), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.043   0.009   PHE A  67 
   TYR   0.087   0.016   TYR A  12 
   ARG   0.073   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.030   0.008   PHE A  67 
   TYR   0.074   0.016   TYR A  12 
   ARG   0.007   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.64
  MolProbity score      =   1.04

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.65
  MolProbity score      =   0.96

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.64
  MolProbity score      =   0.70

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

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


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=  2.796)
  Mean delta:    0.013 (Z=  0.666)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.89     4.71  1.00e+00  2.22e+01   4.7*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    8.009 (Z=  4.707)
  Mean delta:    1.766 (Z=  0.974)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.014
  Max. delta:   75.388
  Mean delta:   11.896

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.244
  Mean delta:    0.083

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.086
  Mean delta:    0.015

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


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

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

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

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

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

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.474
    Angle     :  1.646   8.009   4079  Z= 0.727
    Chirality :  0.083   0.244    176
    Planarity :  0.010   0.064    327
    Dihedral  : 11.066  80.068    769
    Min Nonbonded Distance : 1.722
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    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: -0.68 (0.69), residues: 137
    helix: -0.74 (0.47), residues: 91
    sheet: -0.95 (1.60), residues: 10
    loop :  1.19 (1.22), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.048   0.009   PHE A  67 
   TYR   0.079   0.018   TYR A  12 
   ARG   0.071   0.021   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.032   0.008   PHE A  67 
   TYR   0.067   0.018   TYR A  12 
   ARG   0.007   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.65
  MolProbity score      =   0.54

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.037 (Z=  2.674)
  Mean delta:    0.013 (Z=  0.671)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.14     4.46  1.00e+00  1.99e+01   4.5*sigma
   A 129  ARG  NH1
   A 129  ARG  CZ
   A 129  ARG  NH2       119.30   113.65     5.65  1.30e+00  1.89e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.158 (Z=  4.461)
  Mean delta:    1.794 (Z=  0.996)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   156.37    23.63  5.00e+00  2.23e+01   4.7*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   157.15    22.85  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   158.74    21.26  5.00e+00  1.81e+01   4.3*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   159.17    20.83  5.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.054
  Max. delta:   82.430
  Mean delta:   13.388

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.284
  Mean delta:    0.089

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.478
    Angle     :  1.658   8.158   4079  Z= 0.738
    Chirality :  0.089   0.284    176
    Planarity :  0.011   0.075    327
    Dihedral  : 12.789  82.430    769
    Min Nonbonded Distance : 1.699
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.84 %
      Favored  : 94.16 %
    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: -1.83 (0.67), residues: 137
    helix: -1.55 (0.44), residues: 85
    sheet: -1.36 (1.54), residues: 10
    loop :  0.15 (1.13), residues: 42
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.004   HIS A  43 
   PHE   0.060   0.010   PHE A  67 
   TYR   0.121   0.019   TYR A  91 
   ARG   0.082   0.020   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.004   HIS A  43 
   PHE   0.041   0.011   PHE A  67 
   TYR   0.094   0.021   TYR A  91 
   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:    0.038 (Z=  2.724)
  Mean delta:    0.013 (Z=  0.658)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.92     4.68  1.00e+00  2.19e+01   4.7*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.22     4.38  1.00e+00  1.92e+01   4.4*sigma
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   128.96    -7.26  1.80e+00  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.899 (Z=  4.683)
  Mean delta:    1.780 (Z=  0.983)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.011
  Max. delta:   78.615
  Mean delta:   13.067

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.233
  Mean delta:    0.081

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.097
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.652   7.899   4079  Z= 0.732
    Chirality :  0.081   0.233    176
    Planarity :  0.010   0.072    327
    Dihedral  : 11.895  80.069    769
    Min Nonbonded Distance : 1.689
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.84 %
      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: -1.71 (0.65), residues: 137
    helix: -1.44 (0.42), residues: 93
    sheet: -2.44 (1.12), residues: 10
    loop :  1.07 (1.30), residues: 34
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.047   0.009   PHE A  67 
   TYR   0.091   0.018   TYR A  68 
   ARG   0.080   0.019   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.032   0.009   PHE A  67 
   TYR   0.070   0.019   TYR A  68 
   ARG   0.009   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   1.12

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  94.16 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.66
  MolProbity score      =   0.89

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: 0.85
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.92 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=  2.649)
  Mean delta:    0.013 (Z=  0.662)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.94     4.66  1.00e+00  2.17e+01   4.7*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.75e+01   4.2*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.89     5.31  1.30e+00  1.67e+01   4.1*sigma

  Min. delta:    0.004 (Z=  0.001)
  Max. delta:    8.224 (Z=  4.660)
  Mean delta:    1.831 (Z=  1.012)

                      ----------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   155.50    24.50  5.00e+00  2.40e+01   4.9*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   158.93    21.07  5.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.027
  Max. delta:   75.709
  Mean delta:   13.187

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.231
  Mean delta:    0.087

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.053       0.094       56.48   4.7*sigma

  Min. delta:    0.000
  Max. delta:    0.098
  Mean delta:    0.015

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


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

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

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

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

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

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.471
    Angle     :  1.694   8.224   4079  Z= 0.752
    Chirality :  0.087   0.231    176
    Planarity :  0.011   0.075    327
    Dihedral  : 12.092  89.939    769
    Min Nonbonded Distance : 1.745
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.03 %
      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: -1.66 (0.66), residues: 137
    helix: -1.62 (0.44), residues: 87
    sheet: -1.01 (1.64), residues: 10
    loop :  0.78 (1.10), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.056   0.011   PHE A  67 
   TYR   0.121   0.019   TYR A  91 
   ARG   0.082   0.017   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.039   0.010   PHE A  67 
   TYR   0.094   0.020   TYR A  91 
   ARG   0.007   0.002   ARG A 129 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 68
        1.23 -     1.42: 404
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    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=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.25e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.02e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.01e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.76e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.24 -   106.85: 165
      106.85 -   112.45: 2515
      112.45 -   118.05: 441
      118.05 -   123.66: 822
      123.66 -   129.26: 136
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.91    4.69 1.00e+00 1.00e+00 2.20e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.18    4.42 1.00e+00 1.00e+00 1.95e+01
  angle model="   0" pdb=" CB  HIS A 138 " segid="A   "
        model="   0" pdb=" CG  HIS A 138 " segid="A   "
        model="   0" pdb=" CD2 HIS A 138 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.66    5.54 1.30e+00 5.92e-01 1.81e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.83    5.37 1.30e+00 5.92e-01 1.71e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.78    3.82 1.00e+00 1.00e+00 1.46e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 980
       17.99 -    35.99: 37
       35.99 -    53.98: 11
       53.98 -    71.98: 1
       71.98 -    89.97: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  49 " segid="A   "
           model="   0" pdb=" CG  GLU A  49 " segid="A   "
           model="   0" pdb=" CD  GLU A  49 " segid="A   "
           model="   0" pdb=" OE1 GLU A  49 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.97   89.97     1      3.00e+01 1.11e-03 1.07e+01
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.69   86.69     1      3.00e+01 1.11e-03 1.01e+01
  dihedral model="   0" pdb=" C   GLU A 123 " segid="A   "
           model="   0" pdb=" N   GLU A 123 " segid="A   "
           model="   0" pdb=" CA  GLU A 123 " segid="A   "
           model="   0" pdb=" CB  GLU A 123 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.95    7.35     0      2.50e+00 1.60e-01 8.64e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 85
       0.054 -    0.108: 55
       0.108 -    0.163: 30
       0.163 -    0.217: 4
       0.217 -    0.271: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  GLU A 123 " segid="A   "
            model="   0" pdb=" N   GLU A 123 " segid="A   "
            model="   0" pdb=" C   GLU A 123 " segid="A   "
            model="   0" pdb=" CB  GLU A 123 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  ILE A 122 " segid="A   "
            model="   0" pdb=" N   ILE A 122 " segid="A   "
            model="   0" pdb=" C   ILE A 122 " segid="A   "
            model="   0" pdb=" CB  ILE A 122 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.76e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A  43 " segid="A   "    0.070 2.00e-02 2.50e+03   4.24e-02 3.60e+01
        model="   0" pdb=" CG  HIS A  43 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 " segid="A   "   -0.069 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 " segid="A   "    0.032 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.063 2.00e-02 2.50e+03   3.24e-02 3.14e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.033 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03   3.19e-02 3.04e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.019 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.33: 404
        2.33 -     2.89: 5309
        2.89 -     3.46: 5513
        3.46 -     4.03: 7490
        4.03 -     4.60: 10894
  Nonbonded interactions: 29610
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ3 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.768 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.793 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.798 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.803 1.850
  ... (remaining 29605 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 =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.69
  MolProbity score      =   0.98

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=  2.688)
  Mean delta:    0.013 (Z=  0.665)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.74     4.86  1.00e+00  2.36e+01   4.9*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.088 (Z=  4.860)
  Mean delta:    1.761 (Z=  0.974)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.023
  Max. delta:   79.251
  Mean delta:   12.607

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.231
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.076
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.473
    Angle     :  1.641   8.088   4079  Z= 0.726
    Chirality :  0.082   0.231    176
    Planarity :  0.010   0.057    327
    Dihedral  : 11.517  89.922    769
    Min Nonbonded Distance : 1.713
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    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: -0.91 (0.68), residues: 137
    helix: -1.06 (0.45), residues: 91
    sheet: -1.26 (1.52), residues: 10
    loop :  1.64 (1.21), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.044   0.009   PHE A  67 
   TYR   0.088   0.017   TYR A  68 
   ARG   0.062   0.016   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.030   0.008   PHE A  67 
   TYR   0.068   0.018   TYR A  68 
   ARG   0.006   0.002   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.744)
  Mean delta:    0.013 (Z=  0.664)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.91    -6.51  1.40e+00  2.16e+01   4.7*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.97     4.63  1.00e+00  2.14e+01   4.6*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=  0.001)
  Max. delta:    7.994 (Z=  4.652)
  Mean delta:    1.844 (Z=  1.016)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.007
  Max. delta:   75.105
  Mean delta:   12.780

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.246
  Mean delta:    0.084

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.074
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.472
    Angle     :  1.683   7.994   4079  Z= 0.749
    Chirality :  0.084   0.246    176
    Planarity :  0.009   0.058    327
    Dihedral  : 12.083  80.067    769
    Min Nonbonded Distance : 1.721
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.17 (0.70), residues: 137
    helix: -1.13 (0.46), residues: 89
    sheet: -1.06 (1.76), residues: 10
    loop :  0.89 (1.24), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.024   0.007   PHE A  67 
   TYR   0.070   0.016   TYR A 111 
   ARG   0.065   0.013   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.015   0.005   PHE A  67 
   TYR   0.064   0.017   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 =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.64
  MolProbity score      =   0.66

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.68
  MolProbity score      =   0.74

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   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: ""

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=  2.777)
  Mean delta:    0.013 (Z=  0.662)

                        ----------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=  0.000)
  Max. delta:    8.103 (Z=  4.058)
  Mean delta:    1.766 (Z=  0.976)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.016
  Max. delta:   77.002
  Mean delta:   13.053

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.231
  Mean delta:    0.083

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.111
  Mean delta:    0.016

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.472
    Angle     :  1.646   8.103   4079  Z= 0.728
    Chirality :  0.083   0.231    176
    Planarity :  0.011   0.085    327
    Dihedral  : 11.561  77.002    769
    Min Nonbonded Distance : 1.699
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  4.03 %
      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: -1.19 (0.68), residues: 137
    helix: -1.10 (0.46), residues: 92
    sheet: -1.88 (1.54), residues: 10
    loop :  1.24 (1.21), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.004   HIS A  43 
   PHE   0.041   0.008   PHE A  67 
   TYR   0.121   0.019   TYR A  50 
   ARG   0.092   0.024   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.004   HIS A  43 
   PHE   0.027   0.007   PHE A  67 
   TYR   0.093   0.019   TYR A  50 
   ARG   0.009   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:    0.040 (Z=  3.179)
  Mean delta:    0.013 (Z=  0.671)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.01     4.59  1.00e+00  2.11e+01   4.6*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.856 (Z=  4.593)
  Mean delta:    1.803 (Z=  0.989)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.007
  Max. delta:   75.235
  Mean delta:   12.683

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.249
  Mean delta:    0.086

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.053       0.092       55.40   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.150
  Mean delta:    0.019

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


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

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

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

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

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

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.478
    Angle     :  1.674   7.856   4079  Z= 0.738
    Chirality :  0.086   0.249    176
    Planarity :  0.013   0.113    327
    Dihedral  : 11.743  82.049    769
    Min Nonbonded Distance : 1.725
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    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: -1.56 (0.67), residues: 137
    helix: -1.48 (0.46), residues: 89
    sheet: -1.35 (1.50), residues: 10
    loop :  0.91 (1.14), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.005   HIS A 134 
   PHE   0.060   0.010   PHE A  67 
   TYR   0.115   0.019   TYR A  91 
   ARG   0.120   0.030   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.005   HIS A 134 
   PHE   0.041   0.010   PHE A  67 
   TYR   0.092   0.021   TYR A  91 
   ARG   0.011   0.003   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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


End of input processing

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

   Number of:
     all atoms      : 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=  2.594)
  Mean delta:    0.013 (Z=  0.656)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.91     4.69  1.00e+00  2.20e+01   4.7*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.18     4.42  1.00e+00  1.95e+01   4.4*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.75e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.419 (Z=  4.690)
  Mean delta:    1.756 (Z=  0.970)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   158.92    21.08  5.00e+00  1.78e+01   4.2*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   158.93    21.07  5.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.032
  Max. delta:   79.341
  Mean delta:   12.411

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.251
  Mean delta:    0.081

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.097
  Mean delta:    0.016

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


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

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

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

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

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

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.467
    Angle     :  1.640   7.419   4079  Z= 0.725
    Chirality :  0.081   0.251    176
    Planarity :  0.011   0.073    327
    Dihedral  : 11.509  79.341    769
    Min Nonbonded Distance : 1.692
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  2.42 %
      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: -1.27 (0.70), residues: 137
    helix: -0.99 (0.49), residues: 91
    sheet: -2.03 (1.30), residues: 10
    loop :  0.64 (1.22), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.019   0.004   HIS A  43 
   PHE   0.046   0.009   PHE A  67 
   TYR   0.126   0.019   TYR A  50 
   ARG   0.079   0.023   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.019   0.004   HIS A  43 
   PHE   0.032   0.009   PHE A  67 
   TYR   0.093   0.017   TYR A  50 
   ARG   0.010   0.002   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: ""

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

  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.67
  MolProbity score      =   0.82

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=  2.619)
  Mean delta:    0.013 (Z=  0.668)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 129  ARG  NE
   A 129  ARG  CZ
   A 129  ARG  NH2       119.20   123.71    -4.51  9.00e-01  2.52e+01   5.0*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.85     4.75  1.00e+00  2.26e+01   4.8*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  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:    8.250 (Z=  5.015)
  Mean delta:    1.787 (Z=  0.994)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   80.353
  Mean delta:   12.070

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.257
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.103
  Mean delta:    0.015

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


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

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

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

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

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

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.476
    Angle     :  1.655   8.250   4079  Z= 0.737
    Chirality :  0.082   0.257    176
    Planarity :  0.011   0.079    327
    Dihedral  : 10.983  80.353    769
    Min Nonbonded Distance : 1.749
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    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     : 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: -1.70 (0.66), residues: 137
    helix: -1.64 (0.43), residues: 92
    sheet: -0.43 (1.68), residues: 10
    loop :  0.97 (1.17), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.005   HIS A  43 
   PHE   0.057   0.010   PHE A  67 
   TYR   0.072   0.017   TYR A 111 
   ARG   0.086   0.020   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.015   0.005   HIS A  43 
   PHE   0.039   0.009   PHE A  67 
   TYR   0.065   0.017   TYR A 111 
   ARG   0.006   0.001   ARG A 129 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   0.82

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: ""
  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.64
  MolProbity score      =   1.13

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=  2.722)
  Mean delta:    0.013 (Z=  0.659)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.81     4.79  1.00e+00  2.29e+01   4.8*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.98     4.62  1.00e+00  2.13e+01   4.6*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.60     4.00  1.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.040 (Z=  4.789)
  Mean delta:    1.811 (Z=  1.010)

                      ----------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   156.55    23.45  5.00e+00  2.20e+01   4.7*sigma

  Min. delta:    0.039
  Max. delta:   77.953
  Mean delta:   13.286

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.233
  Mean delta:    0.083

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.055       0.093       60.68   4.7*sigma

  Min. delta:    0.000
  Max. delta:    0.087
  Mean delta:    0.016

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.667   8.040   4079  Z= 0.746
    Chirality :  0.083   0.233    176
    Planarity :  0.011   0.066    327
    Dihedral  : 11.845  77.953    769
    Min Nonbonded Distance : 1.715
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    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: -0.99 (0.68), residues: 137
    helix: -1.06 (0.45), residues: 92
    sheet: -1.62 (1.56), residues: 10
    loop :  1.61 (1.22), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.035   0.007   PHE A  67 
   TYR   0.112   0.018   TYR A  91 
   ARG   0.071   0.020   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.023   0.006   PHE A  67 
   TYR   0.093   0.020   TYR A  91 
   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      : 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=  2.631)
  Mean delta:    0.013 (Z=  0.662)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.98     4.62  1.00e+00  2.13e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.20     4.40  1.00e+00  1.94e+01   4.4*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.86     5.34  1.30e+00  1.69e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.111 (Z=  4.616)
  Mean delta:    1.766 (Z=  0.979)

                      ----------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   146.07    33.93  5.00e+00  4.60e+01   6.8*sigma

  Min. delta:    0.033
  Max. delta:   79.863
  Mean delta:   12.734

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.241
  Mean delta:    0.086

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.079
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.471
    Angle     :  1.653   8.111   4079  Z= 0.731
    Chirality :  0.086   0.241    176
    Planarity :  0.010   0.060    327
    Dihedral  : 11.873  89.958    769
    Min Nonbonded Distance : 1.705
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  4.03 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.22 (0.68), residues: 137
    helix: -1.63 (0.43), residues: 85
    sheet: -1.13 (1.67), residues: 10
    loop :  1.79 (1.14), residues: 42
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.047   0.009   PHE A  67 
   TYR   0.074   0.017   TYR A  50 
   ARG   0.064   0.017   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.032   0.008   PHE A  67 
   TYR   0.059   0.016   TYR A  50 
   ARG   0.006   0.002   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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


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

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.66
  MolProbity score      =   0.70

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

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

  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.67
  MolProbity score      =   0.50

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   0.80

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}

============================== 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: ""

============================== 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: 0.94, per 1000 atoms: 0.42
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (77.239, 47.427, 43.803, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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:    0.037 (Z=  2.651)
  Mean delta:    0.013 (Z=  0.666)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.16     4.44  1.00e+00  1.97e+01   4.4*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.879 (Z=  4.437)
  Mean delta:    1.755 (Z=  0.975)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   75.998
  Mean delta:   14.033

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.236
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.088
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.474
    Angle     :  1.635   7.879   4079  Z= 0.726
    Chirality :  0.082   0.236    176
    Planarity :  0.011   0.067    327
    Dihedral  : 12.321  80.041    769
    Min Nonbonded Distance : 1.728
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  1.61 %
      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: -1.34 (0.66), residues: 137
    helix: -1.22 (0.44), residues: 89
    sheet: -2.59 (1.31), residues: 10
    loop :  1.21 (1.13), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.053   0.009   PHE A  67 
   TYR   0.096   0.019   TYR A  68 
   ARG   0.072   0.021   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.036   0.009   PHE A  67 
   TYR   0.074   0.021   TYR A  68 
   ARG   0.006   0.002   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.63
  MolProbity score      =   1.32

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.614)
  Mean delta:    0.013 (Z=  0.651)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.04     4.56  1.00e+00  2.08e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.17     4.43  1.00e+00  1.96e+01   4.4*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.127 (Z=  4.556)
  Mean delta:    1.794 (Z=  0.971)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   150.57    29.43  5.00e+00  3.46e+01   5.9*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   151.31    28.69  5.00e+00  3.29e+01   5.7*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   155.49    24.51  5.00e+00  2.40e+01   4.9*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   156.88    23.12  5.00e+00  2.14e+01   4.6*sigma
   A 128  MET  CA
   A 128  MET  C
   A 129  ARG  N
   A 129  ARG  CA        180.00   159.81    20.19  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.003
  Max. delta:   77.770
  Mean delta:   12.124

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.232
  Mean delta:    0.083

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.087
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.464
    Angle     :  1.658   8.127   4079  Z= 0.726
    Chirality :  0.083   0.232    176
    Planarity :  0.010   0.066    327
    Dihedral  : 11.690  80.056    769
    Min Nonbonded Distance : 1.735
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  7.30 %
      Allowed  : 10.22 %
      Favored  : 82.48 %
    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: -3.08 (0.68), residues: 137
    helix: -1.93 (0.47), residues: 78
    sheet: -1.76 (1.38), residues: 10
    loop : -1.99 (1.07), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.059   0.010   PHE A  67 
   TYR   0.081   0.015   TYR A  12 
   ARG   0.070   0.016   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.040   0.009   PHE A  67 
   TYR   0.067   0.015   TYR A  12 
   ARG   0.006   0.001   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.665)
  Mean delta:    0.013 (Z=  0.658)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   131.00    -6.60  1.40e+00  2.22e+01   4.7*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.21     4.39  1.00e+00  1.93e+01   4.4*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.230 (Z=  4.717)
  Mean delta:    1.785 (Z=  0.991)

                      ----------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   159.56    20.44  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.019
  Max. delta:   77.738
  Mean delta:   12.379

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.231
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.086
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.656   7.241   4079  Z= 0.736
    Chirality :  0.082   0.231    176
    Planarity :  0.010   0.066    327
    Dihedral  : 11.214  77.738    769
    Min Nonbonded Distance : 1.723
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    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: -0.89 (0.68), residues: 137
    helix: -0.71 (0.46), residues: 92
    sheet: -1.45 (1.39), residues: 10
    loop :  0.72 (1.27), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.043   0.009   PHE A  67 
   TYR   0.076   0.017   TYR A  68 
   ARG   0.075   0.018   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.030   0.008   PHE A  67 
   TYR   0.062   0.017   TYR A  12 
   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: (47.944, 68.682, 54.899, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Ramachandran outliers =   7.30 %
                favored =  82.48 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.66
  MolProbity score      =   1.36

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.753, 42.764, 53.942, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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 =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.66
  MolProbity score      =   0.80

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=  2.597)
  Mean delta:    0.013 (Z=  0.664)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.21     4.39  1.00e+00  1.93e+01   4.4*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.88     5.32  1.30e+00  1.67e+01   4.1*sigma

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:    8.188 (Z=  4.391)
  Mean delta:    1.779 (Z=  0.984)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.034
  Max. delta:   78.602
  Mean delta:   13.811

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.235
  Mean delta:    0.084

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.050       0.089       50.71   4.5*sigma

  Min. delta:    0.000
  Max. delta:    0.080
  Mean delta:    0.015

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.473
    Angle     :  1.647   8.188   4079  Z= 0.731
    Chirality :  0.084   0.235    176
    Planarity :  0.010   0.064    327
    Dihedral  : 12.641  80.042    769
    Min Nonbonded Distance : 1.714
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  1.61 %
      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: -0.86 (0.69), residues: 137
    helix: -0.86 (0.47), residues: 89
    sheet: -1.97 (1.48), residues: 10
    loop :  1.27 (1.18), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.046   0.008   PHE A  67 
   TYR   0.110   0.015   TYR A  91 
   ARG   0.066   0.020   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.031   0.007   PHE A  67 
   TYR   0.089   0.017   TYR A  91 
   ARG   0.005   0.001   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.792)
  Mean delta:    0.013 (Z=  0.650)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.59     4.01  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.772 (Z=  4.008)
  Mean delta:    1.806 (Z=  0.998)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.016
  Max. delta:   88.922
  Mean delta:   13.360

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.225
  Mean delta:    0.084

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  68  TYR  CB
   A  68  TYR  CG
   A  68  TYR  CD1
   A  68  TYR  CD2
   A  68  TYR  CE1
   A  68  TYR  CE2
   A  68  TYR  CZ
   A  68  TYR  OH            0.051       0.098       51.06   4.9*sigma

  Min. delta:    0.000
  Max. delta:    0.079
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.463
    Angle     :  1.670   7.772   4079  Z= 0.741
    Chirality :  0.084   0.225    176
    Planarity :  0.011   0.061    327
    Dihedral  : 12.216  88.922    769
    Min Nonbonded Distance : 1.711
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.81 %
      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: -1.67 (0.66), residues: 137
    helix: -1.57 (0.44), residues: 90
    sheet: -1.98 (1.49), residues: 10
    loop :  1.19 (1.15), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.051   0.010   PHE A  67 
   TYR   0.126   0.019   TYR A  68 
   ARG   0.069   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.035   0.009   PHE A  67 
   TYR   0.098   0.019   TYR A  68 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   0.83

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}
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0090
  RMS(angles)           =   1.67
  MolProbity score      =   0.98

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)----------                  

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: (55.338, 39.485, 87.057, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

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=  2.724)
  Mean delta:    0.013 (Z=  0.660)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.19     4.41  1.00e+00  1.95e+01   4.4*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.091 (Z=  4.411)
  Mean delta:    1.808 (Z=  0.996)

                      ----------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   156.98    23.02  5.00e+00  2.12e+01   4.6*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   158.34    21.66  5.00e+00  1.88e+01   4.3*sigma

  Min. delta:    0.011
  Max. delta:   75.867
  Mean delta:   12.139

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.234
  Mean delta:    0.084

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.082
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.470
    Angle     :  1.673   8.091   4079  Z= 0.741
    Chirality :  0.084   0.234    176
    Planarity :  0.010   0.063    327
    Dihedral  : 11.676  80.055    769
    Min Nonbonded Distance : 1.733
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  3.65 %
      Favored  : 94.89 %
    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: -1.16 (0.67), residues: 137
    helix: -1.07 (0.43), residues: 93
    sheet: -1.40 (1.76), residues: 10
    loop :  1.13 (1.28), residues: 34
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.047   0.009   PHE A  67 
   TYR   0.091   0.018   TYR A  68 
   ARG   0.071   0.016   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.031   0.008   PHE A  67 
   TYR   0.070   0.019   TYR A  68 
   ARG   0.005   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.72
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.81 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:    0.038 (Z=  2.776)
  Mean delta:    0.013 (Z=  0.658)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.93     4.67  1.00e+00  2.19e+01   4.7*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.33     4.27  1.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    8.049 (Z=  4.675)
  Mean delta:    1.767 (Z=  0.983)

                      ----------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   157.42    22.58  5.00e+00  2.04e+01   4.5*sigma

  Min. delta:    0.005
  Max. delta:   78.099
  Mean delta:   12.963

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.241
  Mean delta:    0.082

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.046       0.092       42.03   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.080
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.645   8.049   4079  Z= 0.731
    Chirality :  0.082   0.241    176
    Planarity :  0.010   0.060    327
    Dihedral  : 11.744  79.247    769
    Min Nonbonded Distance : 1.703
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.84 %
      Favored  : 94.16 %
    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: -1.35 (0.67), residues: 137
    helix: -1.24 (0.44), residues: 90
    sheet: -2.34 (1.33), residues: 10
    loop :  1.22 (1.20), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.004   HIS A  43 
   PHE   0.046   0.009   PHE A  67 
   TYR   0.122   0.017   TYR A  50 
   ARG   0.065   0.014   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.004   HIS A  43 
   PHE   0.032   0.008   PHE A  67 
   TYR   0.092   0.017   TYR A  50 
   ARG   0.006   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 60
        1.23 -     1.42: 412
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.46e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.20e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.67e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.54e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.26e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.47 -   105.44: 63
      105.44 -   111.41: 2369
      111.41 -   117.39: 622
      117.39 -   123.36: 841
      123.36 -   129.33: 184
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.86    4.74 1.00e+00 1.00e+00 2.25e+01
  angle model="   0" pdb=" C   LYS A  85 " segid="A   "
        model="   0" pdb=" N   ILE A  86 " segid="A   "
        model="   0" pdb=" CA  ILE A  86 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.70  129.00   -7.30 1.80e+00 3.09e-01 1.65e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.59    4.01 1.00e+00 1.00e+00 1.61e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.33   -4.93 1.40e+00 5.10e-01 1.24e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 955
       16.01 -    32.01: 53
       32.01 -    48.02: 20
       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=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.73   24.27     0      5.00e+00 4.00e-02 2.36e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.02   15.98     0      5.00e+00 4.00e-02 1.02e+01
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.96    7.36     0      2.50e+00 1.60e-01 8.68e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 67
       0.048 -    0.095: 62
       0.095 -    0.143: 36
       0.143 -    0.190: 10
       0.190 -    0.237: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.96e-01
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.56e-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 " segid="A   "    0.123 2.00e-02 2.50e+03   5.42e-02 8.80e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.114 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.024 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.078 2.00e-02 2.50e+03   3.50e-02 3.67e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.015 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane m  Ramachandran outliers =   1.46 %
                favored =  94.89 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.67
  MolProbity score      =   1.01

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
odel="   0" pdb=" CB  TYR A  12 " segid="A   "    0.067 2.00e-02 2.50e+03   3.11e-02 2.89e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.031 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 345
        2.30 -     2.88: 5195
        2.88 -     3.45: 5537
        3.45 -     4.03: 7371
        4.03 -     4.60: 10756
  Nonbonded interactions: 29204
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.738 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.788 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.796 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.807 1.850
  ... (remaining 29199 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.00 %
                favored =  94.16 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.64
  MolProbity score      =   1.05

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  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: 1.18 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)----------                  

  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 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.88e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.71e+00
  bond model="   0" pdb=" CB  THR A  82 " segid="A   "
       model="   0" pdb=" OG1 THR A  82 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.433  1.393  0.040 1.60e-02 3.91e+03 6.36e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.26e+00
  bond model="   0" pdb=" ND1 HIS A 135 " segid="A   "
       model="   0" pdb=" CE1 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.96e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.23 -   106.04: 109
      106.04 -   111.85: 2458
      111.85 -   117.66: 507
      117.66 -   123.47: 843
      123.47 -   129.28: 162
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A 118 " segid="A   "
        model="   0" pdb=" CB  ASP A 118 " segid="A   "
        model="   0" pdb=" CG  ASP A 118 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  117.89   -5.29 1.00e+00 1.00e+00 2.80e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.77    4.83 1.00e+00 1.00e+00 2.33e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.08    4.52 1.00e+00 1.00e+00 2.05e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.79    5.41 1.30e+00 5.92e-01 1.73e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.77    3.83 1.00e+00 1.00e+00 1.47e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.23: 951
       16.23 -    32.45: 52
       32.45 -    48.68: 24
       48.68 -    64.91: 4
       64.91 -    81.13: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LEU A 119 " segid="A   "
           model="   0" pdb=" C   LEU A 119 " segid="A   "
           model="   0" pdb=" N   GLU A 120 " segid="A   "
           model="   0" pdb=" CA  GLU A 120 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.21   19.79     0      5.00e+00 4.00e-02 1.57e+01
  dihedral model="   0" pdb=" CA  PRO A 117 " segid="A   "
           model="   0" pdb=" C   PRO A 117 " segid="A   "
           model="   0" pdb=" N   ASP A 118 " segid="A   "
           model="   0" pdb=" CA  ASP A 118 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.58   18.42     0      5.00e+00 4.00e-02 1.36e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.050: 73
       0.050 -    0.100: 56
       0.100 -    0.149: 38
       0.149 -    0.199: 8
       0.199 -    0.249: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  GLU A 120 " segid="A   "
            model="   0" pdb=" N   GLU A 120 " segid="A   "
            model="   0" pdb=" C   GLU A 120 " segid="A   "
            model="   0" pdb=" CB  GLU A 120 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.14e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.65e-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 " segid="A   "    0.086 2.00e-02 2.50e+03   3.76e-02 4.25e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 " segid="A   "   -0.063 2.00e-02 2.50e+03   3.75e-02 2.81e+01
        model="   0" pdb=" CG  HIS A 139 " segid="A   "    0.059 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 " segid="A   "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 " segid="A   "   -0.033 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.071 2.00e-02 2.50e+03   3.00e-02 2.70e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 337
        2.30 -     2.88: 5162
        2.88 -     3.45: 5499
        3.45 -     4.03: 7310
        4.03 -     4.60: 10678
  Nonbonded interactions: 28986
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.728 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.731 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.794 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.813 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.818 1.850
  ... (remaining 28981 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  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   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 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 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: ""

  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: 1.24 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================


============================== 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=  2.645)
  Mean delta:    0.013 (Z=  0.661)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.99     4.61  1.00e+00  2.12e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.21     4.39  1.00e+00  1.92e+01   4.4*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.012 (Z=  4.606)
  Mean delta:    1.820 (Z=  0.999)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00   153.71    26.29  5.00e+00  2.77e+01   5.3*sigma

  Min. delta:    0.057
  Max. delta:   76.870
  Mean delta:   12.858

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.235
  Mean delta:    0.087

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.085
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.470
    Angle     :  1.680   8.012   4079  Z= 0.743
    Chirality :  0.087   0.235    176
    Planarity :  0.010   0.067    327
    Dihedral  : 11.951  88.024    769
    Min Nonbonded Distance : 1.698
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    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: -1.37 (0.68), residues: 137
    helix: -1.07 (0.45), residues: 86
    sheet: -1.60 (1.60), residues: 10
    loop :  0.20 (1.18), residues: 41
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.042   0.008   PHE A  67 
   TYR   0.074   0.016   TYR A  12 
   ARG   0.070   0.020   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.028   0.007   PHE A  67 
   TYR   0.062   0.016   TYR A  12 
   ARG   0.007   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 81
        1.23 -     1.43: 391
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.47e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.23e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.23e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.61e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.61e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.41 -   106.19: 130
      106.19 -   111.97: 2445
      111.97 -   117.76: 505
      117.76 -   123.54: 847
      123.54 -   129.32: 152
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.30    4.30 1.00e+00 1.00e+00 1.85e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.72    3.88 1.00e+00 1.00e+00 1.51e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.98    3.62 1.00e+00 1.00e+00 1.31e+01
  angle model="   0" pdb=" CA  MET A 128 " segid="A   "
        model="   0" pdb=" C   MET A 128 " segid="A   "
        model="   0" pdb=" N   ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     116.20  123.40   -7.20 2.00e+00 2.50e-01 1.30e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.32   -4.92 1.40e+00 5.10e-01 1.24e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.21: 951
       15.21 -    30.42: 51
       30.42 -    45.63: 18
       45.63 -    60.84: 11
       60.84 -    76.05: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.25   18.75     0      5.00e+00 4.00e-02 1.41e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.19   17.81     0      5.00e+00 4.00e-02 1.27e+01
  dihedral model="   0" pdb=" CA  LEU A 132 " segid="A   "
           model="   0" pdb=" C   LEU A 132 " segid="A   "
           model="   0" pdb=" N   GLU A 133 " segid="A   "
           model="   0" pdb=" CA  GLU A 133 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.24   15.76     0      5.00e+00 4.00e-02 9.93e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 63
       0.048 -    0.095: 66
       0.095 -    0.143: 35
       0.143 -    0.191: 10
       0.191 -    0.238: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    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  LEU A 132 " segid="A   "
            model="   0" pdb=" N   LEU A 132 " segid="A   "
            model="   0" pdb=" C   LEU A 132 " segid="A   "
            model="   0" pdb=" CB  LEU A 132 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.68e-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 " segid="A   "    0.095 2.00e-02 2.50e+03   4.23e-02 5.36e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.088 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.034 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.068 2.00e-02 2.50e+03   3.11e-02 2.90e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  67 " segid="A   "    0.075 2.00e-02 2.50e+03   2.89e-02 2.50e+01
        model="   0" pdb=" CG  PHE A  67 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  67 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  67 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  67 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  67 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  67 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  67 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  67 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  67 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  67 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  67 " segid="A   "    0.035 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.28: 271
        2.28 -     2.86: 5087
        2.86 -     3.44: 5674
        3.44 -     4.02: 7515
        4.02 -     4.60: 10993
  Nonbonded interactions: 29540
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.694 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.720 1.850
  nonbonded model="   0" pdb=" H2  MET A   1 " segid="A   "
            model="   0" pdb=" OE1 GLU A 123 " segid="A   "
     model   vdw
     1.736 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.780 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.800 1.850
  ... (remaining 29535 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 =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.68
  MolProbity score      =   0.96

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=  2.745)
  Mean delta:    0.013 (Z=  0.667)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   130.02    -8.32  1.80e+00  2.13e+01   4.6*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.317 (Z=  4.620)
  Mean delta:    1.798 (Z=  0.994)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   157.29    22.71  5.00e+00  2.06e+01   4.5*sigma

  Min. delta:    0.021
  Max. delta:   77.535
  Mean delta:   13.370

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.256
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.082
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.475
    Angle     :  1.668   8.317   4079  Z= 0.739
    Chirality :  0.081   0.256    176
    Planarity :  0.010   0.063    327
    Dihedral  : 11.746  80.063    769
    Min Nonbonded Distance : 1.698
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.65 (0.67), residues: 137
    helix: -1.70 (0.45), residues: 84
    sheet: -2.23 (1.52), residues: 10
    loop :  1.14 (1.07), residues: 43
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.003   HIS A  43 
   PHE   0.050   0.009   PHE A  67 
   TYR   0.082   0.017   TYR A  68 
   ARG   0.071   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.003   HIS A  43 
   PHE   0.033   0.009   PHE A  67 
   TYR   0.064   0.018   TYR A  68 
   ARG   0.005   0.002   ARG A  58 

                     ----------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: 0.92
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.01 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  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: 0.01s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   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)----------                  

  Ramachandran outliers =   0.73 %
                favored =  94.16 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.67
  MolProbity score      =   1.55

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 76
        1.23 -     1.43: 396
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.31e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.11e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.08e+00
  bond model="   0" pdb=" CZ  ARG A  58 " segid="A   "
       model="   0" pdb=" NH2 ARG A  58 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.00e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.63e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.74 -   106.41: 152
      106.41 -   112.08: 2446
      112.08 -   117.75: 499
      117.75 -   123.42: 803
      123.42 -   129.09: 179
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.92    4.68 1.00e+00 1.00e+00 2.19e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.81    3.79 1.00e+00 1.00e+00 1.44e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.29    4.91 1.30e+00 5.92e-01 1.43e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.75    4.45 1.30e+00 5.92e-01 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.35: 936
       15.35 -    30.70: 72
       30.70 -    46.04: 16
       46.04 -    61.39: 7
       61.39 -    76.74: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A 125 " segid="A   "
           model="   0" pdb=" C   LYS A 125 " segid="A   "
           model="   0" pdb=" N   VAL A 126 " segid="A   "
           model="   0" pdb=" CA  VAL A 126 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  136.61   43.39     0      5.00e+00 4.00e-02 7.53e+01
  dihedral model="   0" pdb=" CA  ASP A 118 " segid="A   "
           model="   0" pdb=" C   ASP A 118 " segid="A   "
           model="   0" pdb=" N   LEU A 119 " segid="A   "
           model="   0" pdb=" CA  LEU A 119 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.24   33.76     0      5.00e+00 4.00e-02 4.56e+01
  dihedral model="   0" pdb=" CA  HIS A 138 " segid="A   "
           model="   0" pdb=" C   HIS A 138 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.35   26.65     0      5.00e+00 4.00e-02 2.84e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 67
       0.050 -    0.100: 60
       0.100 -    0.149: 42
       0.149 -    0.199: 5
       0.199 -    0.249: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  VAL A 126 " segid="A   "
            model="   0" pdb=" N   VAL A 126 " segid="A   "
            model="   0" pdb=" C   VAL A 126 " segid="A   "
            model="   0" pdb=" CB  VAL A 126 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    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  68 " segid="A   "    0.048 2.00e-02 2.50e+03   3.56e-02 3.81e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.092 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.050 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.035 2.00e-02 2.50e+03   3.53e-02 3.73e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.074 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.024 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.074 2.00e-02 2.50e+03   3.33e-02 3.34e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.069 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.030 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.29: 310
        2.29 -     2.87: 5172
        2.87 -     3.45: 5385
        3.45 -     4.02: 7164
        4.02 -     4.60: 10508
  Nonbonded interactions: 28539
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.739 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.779 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.789 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.799 1.850
  ... (remaining 28534 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}

  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: ""
        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 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}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.072, 40.681, 71.712, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.721)
  Mean delta:    0.013 (Z=  0.663)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.09     4.51  1.00e+00  2.04e+01   4.5*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.115 (Z=  4.514)
  Mean delta:    1.793 (Z=  0.987)

                      ----------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   148.60    31.40  5.00e+00  3.94e+01   6.3*sigma

  Min. delta:    0.020
  Max. delta:   77.217
  Mean delta:   12.890

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.245
  Mean delta:    0.083

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.082
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.472
    Angle     :  1.668   8.115   4079  Z= 0.736
    Chirality :  0.083   0.245    176
    Planarity :  0.011   0.063    327
    Dihedral  : 11.584  89.935    769
    Min Nonbonded Distance : 1.696
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.92 %
      Favored  : 96.35 %
    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 : 0.76 %
  
  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: -0.54 (0.68), residues: 137
    helix: -0.85 (0.46), residues: 89
    sheet: -0.26 (1.92), residues: 10
    loop :  1.54 (1.13), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.033   0.008   PHE A  67 
   TYR   0.088   0.019   TYR A  50 
   ARG   0.072   0.020   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.024   0.007   PHE A  67 
   TYR   0.071   0.021   TYR A  50 
   ARG   0.009   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 1.05, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (66.731, 38.24, 50.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: ""

  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)----------                  

  Time building chain proxies: 0.91, per 1000 atoms: 0.41
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.167, 78.292, 51.068, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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 =  96.35 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.67
  MolProbity score      =   1.06

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}

  Symmetric amino acids flipped
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   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:    0.040 (Z=  2.724)
  Mean delta:    0.013 (Z=  0.668)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.18     4.42  1.00e+00  1.96e+01   4.4*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.99     5.21  1.30e+00  1.60e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.068 (Z=  4.423)
  Mean delta:    1.807 (Z=  1.004)

                      ----------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   151.48    28.52  5.00e+00  3.25e+01   5.7*sigma

  Min. delta:    0.007
  Max. delta:   78.813
  Mean delta:   13.272

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.239
  Mean delta:    0.084

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.119
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.476
    Angle     :  1.674   8.068   4079  Z= 0.745
    Chirality :  0.084   0.239    176
    Planarity :  0.012   0.088    327
    Dihedral  : 11.895  79.936    769
    Min Nonbonded Distance : 1.668
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.57 (0.66), residues: 137
    helix: -1.47 (0.43), residues: 87
    sheet: -1.75 (1.56), residues: 10
    loop :  0.84 (1.14), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.050   0.010   PHE A  67 
   TYR   0.147   0.021   TYR A  91 
   ARG   0.095   0.026   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.034   0.009   PHE A  67 
   TYR   0.118   0.023   TYR A  91 
   ARG   0.013   0.003   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.935, 70.533, 45.126, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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=  0.003)
  Max. delta:    0.039 (Z=  2.723)
  Mean delta:    0.013 (Z=  0.661)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   117.50     5.10  1.00e+00  2.60e+01   5.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.90     4.70  1.00e+00  2.21e+01   4.7*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.89     5.31  1.30e+00  1.67e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.809 (Z=  5.101)
  Mean delta:    1.839 (Z=  1.009)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   134.61    45.39  5.00e+00  8.24e+01   9.1*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   153.98    26.02  5.00e+00  2.71e+01   5.2*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   155.92    24.08  5.00e+00  2.32e+01   4.8*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00  -159.01   -20.99  5.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.032
  Max. delta:   78.391
  Mean delta:   12.620

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.305
  Mean delta:    0.090

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.083
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.471
    Angle     :  1.698   7.809   4079  Z= 0.750
    Chirality :  0.090   0.305    176
    Planarity :  0.010   0.063    327
    Dihedral  : 11.286  80.051    769
    Min Nonbonded Distance : 1.728
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  6.57 %
      Favored  : 90.51 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  3.23 %
      Favored  : 96.77 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.62 (0.72), residues: 137
    helix: -1.67 (0.49), residues: 70
    sheet: -1.67 (1.31), residues: 10
    loop :  0.19 (1.03), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.053   0.009   PHE A  67 
   TYR   0.090   0.016   TYR A  68 
   ARG   0.070   0.018   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.036   0.009   PHE A  67 
   TYR   0.070   0.017   TYR A  68 
   ARG   0.005   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.67
  MolProbity score      =   1.02

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.92 %
                favored =  90.51 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     1
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.70
  MolProbity score      =   1.03

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.66, per 1000 atoms: 0.30
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.53, 53.278, 67.581, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: (55.039, 43.969, 44.068, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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}

  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: {'PTRANS': 7, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.744)
  Mean delta:    0.013 (Z=  0.658)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.86     4.74  1.00e+00  2.24e+01   4.7*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.34     4.26  1.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:    8.081 (Z=  4.738)
  Mean delta:    1.780 (Z=  0.981)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.010
  Max. delta:   76.727
  Mean delta:   12.366

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.246
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.083
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.652   8.081   4079  Z= 0.731
    Chirality :  0.082   0.246    176
    Planarity :  0.010   0.063    327
    Dihedral  : 11.032  76.727    769
    Min Nonbonded Distance : 1.707
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -0.80 (0.67), residues: 137
    helix: -0.70 (0.45), residues: 90
    sheet: -2.91 (1.07), residues: 10
    loop :  1.33 (1.18), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.024   0.007   PHE A  67 
   TYR   0.072   0.016   TYR A  68 
   ARG   0.068   0.020   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.018   0.005   PHE A  67 
   TYR   0.058   0.018   TYR A  12 
   ARG   0.007   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================


============================== 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 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: ""
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}
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   1.35
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.65
  MolProbity score      =   1.11

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.67, per 1000 atoms: 0.30
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.027, 48.151, 52.528, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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:    0.037 (Z=  2.620)
  Mean delta:    0.013 (Z=  0.654)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.81     4.79  1.00e+00  2.30e+01   4.8*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.50    -6.10  1.40e+00  1.90e+01   4.4*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.75e+01   4.2*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    7.060 (Z=  4.793)
  Mean delta:    1.761 (Z=  0.979)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.131
  Max. delta:   76.579
  Mean delta:   12.706

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.233
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.083
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.466
    Angle     :  1.635   7.060   4079  Z= 0.727
    Chirality :  0.081   0.233    176
    Planarity :  0.010   0.064    327
    Dihedral  : 11.754  80.023    769
    Min Nonbonded Distance : 1.712
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.07 (0.69), residues: 137
    helix: -0.84 (0.46), residues: 93
    sheet: -2.46 (1.36), residues: 10
    loop :  1.01 (1.29), residues: 34
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.043   0.009   PHE A  67 
   TYR   0.072   0.016   TYR A  12 
   ARG   0.072   0.018   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.029   0.008   PHE A  67 
   TYR   0.061   0.017   TYR A  12 
   ARG   0.007   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.166, 61.349, 50.39, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.04, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (74.398, 42.82, 45.697, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: (48.616, 59.472, 39.911, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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 =  96.35 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.64
  MolProbity score      =   0.74

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: {'PTRANS': 7, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A 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)----------                  


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   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: 0.56
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.65 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (61.056, 48.761, 38.077, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A 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}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     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=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.98e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.69e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.63e+00
  bond model="   0" pdb=" CE1 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.50e+00
  bond model="   0" pdb=" CB  THR A  83 " segid="A   "
       model="   0" pdb=" OG1 THR A  83 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.433  1.390  0.043 1.60e-02 3.91e+03 7.37e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.39 -   105.08: 45
      105.08 -   110.76: 2259
      110.76 -   116.45: 706
      116.45 -   122.13: 678
      122.13 -   127.82: 391
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.29    5.91 1.30e+00 5.92e-01 2.07e+01
  angle model="   0" pdb=" CB  HIS A 139 " segid="A   "
        model="   0" pdb=" CG  HIS A 139 " segid="A   "
        model="   0" pdb=" CD2 HIS A 139 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.56    5.64 1.30e+00 5.92e-01 1.88e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.63    3.97 1.00e+00 1.00e+00 1.57e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.13    5.07 1.30e+00 5.92e-01 1.52e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.43: 984
       16.43 -    32.85: 31
       32.85 -    49.28: 16
       49.28 -    65.70: 0
       65.70 -    82.13: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   82.13  -82.13     1      3.00e+01 1.11e-03 9.21e+00
  dihedral model="   0" pdb=" C   ILE A  77 " segid="A   "
           model="   0" pdb=" N   ILE A  77 " segid="A   "
           model="   0" pdb=" CA  ILE A  77 " segid="A   "
           model="   0" pdb=" CB  ILE A  77 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -129.49    7.49     0      2.50e+00 1.60e-01 8.98e+00
  dihedral model="   0" pdb=" C   ASP A  44 " segid="A   "
           model="   0" pdb=" N   ASP A  44 " segid="A   "
           model="   0" pdb=" CA  ASP A  44 " segid="A   "
           model="   0" pdb=" CB  ASP A  44 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.39    6.79     0      2.50e+00 1.60e-01 7.37e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 73
       0.047 -    0.093: 58
       0.093 -    0.140: 33
       0.140 -    0.186: 8
       0.186 -    0.233: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality model="   0" pdb=" CA  ARG A 127 " segid="A   "
            model="   0" pdb=" N   ARG A 127 " segid="A   "
            model="   0" pdb=" C   ARG A 127 " segid="A   "
            model="   0" pdb=" CB  ARG A 127 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.83e-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 " segid="A   "   -0.064 2.00e-02 2.50e+03   3.77e-02 4.27e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.078 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.038 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 137 " segid="A   "    0.074 2.00e-02 2.50e+03   4.44e-02 3.94e+01
        model="   0" pdb=" CG  HIS A 137 " segid="A   "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 137 " segid="A   "   -0.069 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 137 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 137 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 137 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 137 " segid="A   "    0.044 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 135 " segid="A   "   -0.068 2.00e-02 2.50e+03   4.24e-02 3.59e+01
        model="   0" pdb=" CG  HIS A 135 " segid="A   "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 135 " segid="A   "    0.070 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 135 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 135 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 135 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 135 " segid="A   "   -0.047 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.33: 435
        2.33 -     2.90: 5339
        2.90 -     3.47: 5540
        3.47 -     4.03: 7557
        4.03 -     4.60: 10939
  Nonbonded interactions: 29810
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A 120 " segid="A   "
            model="   0" pdb=" HG  SER A 130 " segid="A   "
     model   vdw
     1.763 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.779 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.799 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.828 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.846 1.730
  ... (remaining 29805 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=  2.693)
  Mean delta:    0.013 (Z=  0.655)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   117.87     4.73  1.00e+00  2.24e+01   4.7*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.84     5.36  1.30e+00  1.70e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.959 (Z=  4.734)
  Mean delta:    1.778 (Z=  0.990)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.010
  Max. delta:   84.531
  Mean delta:   14.090

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.227
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.106
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.466
    Angle     :  1.649   7.959   4079  Z= 0.735
    Chirality :  0.081   0.227    176
    Planarity :  0.011   0.081    327
    Dihedral  : 12.345  84.531    769
    Min Nonbonded Distance : 1.733
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    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: -0.85 (0.69), residues: 137
    helix: -1.06 (0.46), residues: 91
    sheet: -1.32 (1.59), residues: 10
    loop :  1.81 (1.25), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A  43 
   PHE   0.046   0.009   PHE A  67 
   TYR   0.075   0.016   TYR A  12 
   ARG   0.088   0.019   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A  43 
   PHE   0.031   0.008   PHE A  67 
   TYR   0.062   0.016   TYR A  12 
   ARG   0.006   0.002   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}
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (58.834, 47.582, 48.334, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: (43.261, 74.142, 50.049, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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 =  95.62 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.65
  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: 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.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 56
        1.23 -     1.42: 416
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.77e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.60e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    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=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    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 " segid="A   "
       model="   0" pdb=" NH1 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.323  1.289  0.034 1.40e-02 5.10e+03 5.76e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.22 -   105.33: 51
      105.33 -   111.45: 2417
      111.45 -   117.56: 609
      117.56 -   123.68: 873
      123.68 -   129.79: 129
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.06    4.54 1.00e+00 1.00e+00 2.06e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.90    5.30 1.30e+00 5.92e-01 1.66e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.05    5.15 1.30e+00 5.92e-01 1.57e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.07    5.13 1.30e+00 5.92e-01 1.56e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.79   -5.39 1.40e+00 5.10e-01 1.48e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 975
       17.44 -    34.89: 39
       34.89 -    52.33: 13
       52.33 -    69.78: 3
       69.78 -    87.22: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  51 " segid="A   "
           model="   0" pdb=" C   ILE A  51 " segid="A   "
           model="   0" pdb=" N   PRO A  52 " segid="A   "
           model="   0" pdb=" CA  PRO A  52 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.33   21.67     0      5.00e+00 4.00e-02 1.88e+01
  dihedral model="   0" pdb=" CB  GLU A 120 " segid="A   "
           model="   0" pdb=" CG  GLU A 120 " segid="A   "
           model="   0" pdb=" CD  GLU A 120 " segid="A   "
           model="   0" pdb=" OE1 GLU A 120 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.22   87.22     1      3.00e+01 1.11e-03 1.02e+01
  dihedral model="   0" pdb=" C   VAL A  41 " segid="A   "
           model="   0" pdb=" N   VAL A  41 " segid="A   "
           model="   0" pdb=" CA  VAL A  41 " segid="A   "
           model="   0" pdb=" CB  VAL A  41 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -129.37    7.37     0      2.50e+00 1.60e-01 8.68e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.048: 78
       0.048 -    0.094: 61
       0.094 -    0.141: 25
       0.141 -    0.188: 9
       0.188 -    0.234: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  90 " segid="A   "
            model="   0" pdb=" N   SER A  90 " segid="A   "
            model="   0" pdb=" C   SER A  90 " segid="A   "
            model="   0" pdb=" CB  SER A  90 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.18e-01
  chirality model="   0" pdb=" CA  VAL A  41 " segid="A   "
            model="   0" pdb=" N   VAL A  41 " segid="A   "
            model="   0" pdb=" C   VAL A  41 " segid="A   "
            model="   0" pdb=" CB  VAL A  41 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.25    0.19 2.00e-01 2.50e+01 8.82e-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 " segid="A   "   -0.012 2.00e-02 2.50e+03   4.71e-02 6.66e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.104 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.055 2.00e-02 2.50e+03   2.83e-02 2.40e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 " segid="A   "    0.071 2.00e-02 2.50e+03   2.79e-02 2.33e+01
        model="   0" pdb=" CG  TYR A  81 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 " segid="A   "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 " segid="A   "   -0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 285
        2.28 -     2.86: 5204
        2.86 -     3.44: 5728
        3.44 -     4.02: 7565
        4.02 -     4.60: 11355
  Nonbonded interactions: 30137
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.701 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.782 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A 113 " segid="A   "
            model="   0" pdb=" OE2 GLU A 120 " segid="A   "
     model   vdw
     1.782 1.730
  nonbonded model="   0" pdb=" HZ3 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.810 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.824 1.850
  ... (remaining 30132 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (76.375, 61.153, 43.594, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 0.59
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.67 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        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: 0.67
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.77 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   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: 1.05
  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)----------                  


  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.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 128
        1.23 -     1.43: 344
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.11e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.84e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.65e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.56e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.29e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.14 -   106.24: 132
      106.24 -   112.35: 2523
      112.35 -   118.45: 490
      118.45 -   124.56: 850
      124.56 -   130.66: 84
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.66   -6.26 1.40e+00 5.10e-01 2.00e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.33    4.27 1.00e+00 1.00e+00 1.82e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      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=" CA  ASP A  47 " segid="A   "
        model="   0" pdb=" CB  ASP A  47 " segid="A   "
        model="   0" pdb=" CG  ASP A  47 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.39   -3.79 1.00e+00 1.00e+00 1.43e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.57: 954
       15.57 -    31.14: 50
       31.14 -    46.71: 19
       46.71 -    62.28: 8
       62.28 -    77.84: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.98   21.02     0      5.00e+00 4.00e-02 1.77e+01
  dihedral model="   0" pdb=" CA  GLY A 121 " segid="A   "
           model="   0" pdb=" C   GLY A 121 " segid="A   "
           model="   0" pdb=" N   ILE A 122 " segid="A   "
           model="   0" pdb=" CA  ILE A 122 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.67  -20.33     0      5.00e+00 4.00e-02 1.65e+01
  dihedral model="   0" pdb=" CA  GLU A 120 " segid="A   "
           model="   0" pdb=" 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: 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  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.96e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.85e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.38e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.93e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.86e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.89 -   106.57: 156
      106.57 -   112.24: 2478
      112.24 -   117.91: 458
      117.91 -   123.58: 845
      123.58 -   129.26: 142
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.79    4.81 1.00e+00 1.00e+00 2.31e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.07    5.13 1.30e+00 5.92e-01 1.55e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      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=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.59    4.61 1.30e+00 5.92e-01 1.26e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 953
       16.01 -    32.03: 54
       32.03 -    48.04: 19
       48.04 -    64.06: 4
       64.06 -    80.07: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.09   17.91     0      5.00e+00 4.00e-02 1.28e+01
  dihedral model="   0" pdb=" CB  MET A 128 " segid="A   "
           model="   0" pdb=" CG  MET A 128 " segid="A   "
           model="   0" pdb=" SD  MET A 128 " segid="A   "
           model="   0" pdb=" CE  MET A 128 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.08  -59.92     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   0" pdb=" N   HIS A 135 " segid="A   "
           model="   0" pdb=" C   GLU A 120 " segid="A   "
           model="   0" pdb=" N   GLY A 121 " segid="A   "
           model="   0" pdb=" CA  GLY A 121 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.36  -19.64     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 65
       0.046 -    0.091: 60
       0.091 -    0.136: 29
       0.136 -    0.180: 19
       0.180 -    0.225: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    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  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.68e-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 " segid="A   "   -0.076 2.00e-02 2.50e+03   3.49e-02 3.65e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.074 2.00e-02 2.50e+03   3.16e-02 2.99e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane CA  HIS A 135 " segid="A   "
           model="   0" pdb=" CB  HIS A 135 " segid="A   "
           model="   0" pdb=" CG  HIS A 135 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.77  -58.23     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.048: 69
       0.048 -    0.095: 59
       0.095 -    0.142: 37
       0.142 -    0.189: 9
       0.189 -    0.237: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.85e-01
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.30e-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 " segid="A   "   -0.081 2.00e-02 2.50e+03   3.53e-02 3.73e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.027 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.066 2.00e-02 2.50e+03   3.20e-02 3.08e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane mmodel="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.046 2.00e-02 2.50e+03   2.57e-02 1.99e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.29: 313
        2.29 -     2.87: 5157
        2.87 -     3.45: 5535
        3.45 -     4.02: 7353
        4.02 -     4.60: 10829
  Nonbonded interactions: 29187
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.754 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.765 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.798 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.816 1.850
  ... (remaining 29182 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
odel="   0" pdb=" CB  HIS A  43 " segid="A   "   -0.042 2.00e-02 2.50e+03   2.64e-02 1.40e+01
        model="   0" pdb=" CG  HIS A  43 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 " segid="A   "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 " segid="A   "   -0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 279
        2.29 -     2.86: 5160
        2.86 -     3.44: 5457
        3.44 -     4.02: 7235
        4.02 -     4.60: 10696
  Nonbonded interactions: 28827
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.708 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.784 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.798 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.802 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.803 1.850
  ... (remaining 28822 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 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 -     1.04: 1106
        1.04 -     1.23: 74
        1.23 -     1.43: 398
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.06e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    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=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.12e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.86e+00
  bond model="   0" pdb=" ND1 HIS A 136 " segid="A   "
       model="   0" pdb=" CE1 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.41e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.74 -   105.11: 43
      105.11 -   111.49: 2417
      111.49 -   117.86: 632
      117.86 -   124.23: 890
      124.23 -   130.60: 97
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.60   -6.20 1.40e+00 5.10e-01 1.96e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.47    5.73 1.30e+00 5.92e-01 1.94e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CB  ASP A  36 " segid="A   "
        model="   0" pdb=" CG  ASP A  36 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.71   -4.11 1.00e+00 1.00e+00 1.69e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.57   -5.17 1.40e+00 5.10e-01 1.36e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 988
       17.94 -    35.88: 26
       35.88 -    53.82: 14
       53.82 -    71.76: 2
       71.76 -    89.70: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.95   22.05     0      5.00e+00 4.00e-02 1.95e+01
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.70   89.70     1      3.00e+01 1.11e-03 1.06e+01
  dihedral model="   0" pdb=" CB  GLU A  32 " segid="A   "
           model="   0" pdb=" CG  GLU A  32 " segid="A   "
           model="   0" pdb=" CD  GLU A  32 " segid="A   "
           model="   0" pdb=" OE1 GLU A  32 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.13   87.13     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 81
       0.052 -    0.104: 55
       0.104 -    0.156: 33
       0.156 -    0.207: 5
       0.207 -    0.259: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality model="   0" pdb=" CA  HIS A 134 " segid="A   "
            model="   0" pdb=" N   HIS A 134 " segid="A   "
            model="   0" pdb=" C   HIS A 134 " segid="A   "
            model="   0" pdb=" CB  HIS A 134 " segid="A   "
    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  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    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 " segid="A   "    0.083 2.00e-02 2.50e+03   3.37e-02 3.42e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.064 2.00e-02 2.50e+03   3.13e-02 2.94e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.037 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "    0.066 2.00e-02 2.50e+03   3.05e-02 2.80e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.035 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 324
        2.30 -     2.87: 5191
        2.87 -     3.45: 5526
        3.45 -     4.02: 7400
        4.02 -     4.60: 10849
  Nonbonded interactions: 29290
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.787 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.791 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.797 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HH  TYR A  68 " segid="A   "
     model   vdw
     1.799 1.730
  ... (remaining 29285 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 62
        1.23 -     1.42: 410
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 9.97e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.30e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.21e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.73e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.64e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.87 -   106.15: 115
      106.15 -   112.42: 2548
      112.42 -   118.69: 492
      118.69 -   124.97: 863
      124.97 -   131.24: 61
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.08    5.52 1.00e+00 1.00e+00 3.05e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  131.24   -6.84 1.40e+00 5.10e-01 2.39e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.20    4.40 1.00e+00 1.00e+00 1.94e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.96   -5.56 1.40e+00 5.10e-01 1.58e+01
  angle model="   0" pdb=" NH1 ARG A 127 " segid="A   "
        model="   0" pdb=" CZ  ARG A 127 " segid="A   "
        model="   0" pdb=" NH2 ARG A 127 " segid="A   "
      ideal   model   delta    sigma   weight residual
     119.30  114.33    4.97 1.30e+00 5.92e-01 1.46e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 957
       16.01 -    32.03: 50
       32.03 -    48.04: 17
       48.04 -    64.06: 6
       64.06 -    80.07: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.81   16.19     0      5.00e+00 4.00e-02 1.05e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.21   15.79     0      5.00e+00 4.00e-02 9.98e+00
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.98    7.38     0      2.50e+00 1.60e-01 8.72e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 72
       0.047 -    0.094: 56
       0.094 -    0.141: 31
       0.141 -    0.187: 15
       0.187 -    0.234: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.81e-01
  chirality model="   0" pdb=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.05e-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 " segid="A   "   -0.051 2.00e-02 2.50e+03   3.30e-02 3.26e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.071 2.00e-02 2.50e+03   3.13e-02 2.94e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.064 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.050 2.00e-02 2.50e+03   2.60e-02 2.02e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.40 -     2.04: 39
        2.04 -     2.68: 3164
        2.68 -     3.32: 6557
        3.32 -     3.96: 7881
        3.96 -     4.60: 11787
  Nonbonded interactions: 29428
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  38 " segid="A   "
            model="   0" pdb="HH21 ARG A 127 " segid="A   "
     model   vdw
     1.401 2.270
  nonbonded model="   0" pdb="HG23 THR A  82 " segid="A   "
            model="   0" pdb=" H   THR A  92 " segid="A   "
     model   vdw
     1.626 2.270
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.707 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.745 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.759 1.850
  ... (remaining 29423 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.941, 55.467, 49.538, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: (47.785, 37.056, 62.524, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.72
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.82 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================


============================== 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 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 -     1.04: 1106
        1.04 -     1.23: 100
        1.23 -     1.43: 372
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.08e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.73e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.37e+00
  bond model="   0" pdb=" CB  THR A  82 " segid="A   "
       model="   0" pdb=" OG1 THR A  82 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.433  1.393  0.040 1.60e-02 3.91e+03 6.32e+00
  bond model="   0" pdb=" CE1 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.68e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.30 -   106.08: 112
      106.08 -   111.86: 2448
      111.86 -   117.64: 516
      117.64 -   123.42: 833
      123.42 -   129.21: 170
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.94    4.66 1.00e+00 1.00e+00 2.17e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.21   -4.81 1.40e+00 5.10e-01 1.18e+01
  angle model="   0" pdb=" CB  HIS A 138 " segid="A   "
        model="   0" pdb=" CG  HIS A 138 " segid="A   "
        model="   0" pdb=" CD2 HIS A 138 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.80    4.40 1.30e+00 5.92e-01 1.14e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.31    3.29 1.00e+00 1.00e+00 1.08e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.64: 947
       15.64 -    31.28: 59
       31.28 -    46.92: 21
       46.92 -    62.57: 4
       62.57 -    78.21: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A 122 " segid="A   "
           model="   0" pdb=" C   ILE A 122 " segid="A   "
           model="   0" pdb=" N   GLU A 123 " segid="A   "
           model="   0" pdb=" CA  GLU A 123 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.49   34.51     0      5.00e+00 4.00e-02 4.76e+01
  dihedral model="   0" pdb=" CA  LYS A 125 " segid="A   "
           model="   0" pdb=" C   LYS A 125 " segid="A   "
           model="   0" pdb=" N   VAL A 126 " segid="A   "
           model="   0" pdb=" CA  VAL A 126 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.37   23.63     0      5.00e+00 4.00e-02 2.23e+01
  dihedral model="   0" pdb=" CA  ALA A 124 " segid="A   "
           model="   0" pdb=" C   ALA A 124 " segid="A   "
           model="   0" pdb=" N   LYS A 125 " segid="A   "
           model="   0" pdb=" CA  LYS A 125 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.37   17.63     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 69
       0.047 -    0.095: 54
       0.095 -    0.142: 39
       0.142 -    0.189: 12
       0.189 -    0.236: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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=" CB  ILE A 122 " segid="A   "
            model="   0" pdb=" CA  ILE A 122 " segid="A   "
            model="   0" pdb=" CG1 ILE A 122 " segid="A   "
            model="   0" pdb=" CG2 ILE A 122 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 8.05e-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 " segid="A   "    0.053 2.00e-02 2.50e+03   3.70e-02 4.10e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.095 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.049 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.034 2.00e-02 2.50e+03   3.35e-02 3.37e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.051 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.062 2.00e-02 2.50e+03   3.14e-02 2.95e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 344
        2.30 -     2.88: 5159
        2.88 -     3.45: 5445
        3.45 -     4.03: 7310
        4.03 -     4.60: 10650
  Nonbonded interactions: 28908
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.748 1.850
  nonbonded model="   0" pdb=" OE1 GLU A 123 " segid="A   "
            model="   0" pdb=" HZ2 LYS A 125 " segid="A   "
     model   vdw
     1.761 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.773 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.797 1.730
  ... (remaining 28903 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.341, 57.157, 46.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.03
  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.


============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 56
        1.23 -     1.42: 416
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.48e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.92e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.47e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.44e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.23e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.55 -   105.55: 70
      105.55 -   111.55: 2404
      111.55 -   117.55: 594
      117.55 -   123.56: 863
      123.56 -   129.56: 148
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.91    4.69 1.00e+00 1.00e+00 2.20e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.56   -5.16 1.40e+00 5.10e-01 1.36e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.08    3.52 1.00e+00 1.00e+00 1.24e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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 -    15.61: 948
       15.61 -    31.23: 61
       31.23 -    46.84: 16
       46.84 -    62.45: 5
       62.45 -    78.06: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.97   33.03     0      5.00e+00 4.00e-02 4.36e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      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  TYR A  81 " segid="A   "
           model="   0" pdb=" C   TYR A  81 " segid="A   "
           model="   0" pdb=" N   THR A  82 " segid="A   "
           model="   0" pdb=" CA  THR A  82 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.13   17.87     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 61
       0.046 -    0.091: 61
       0.091 -    0.137: 37
       0.137 -    0.183: 15
       0.183 -    0.229: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.95e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.53e-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 " segid="A   "   -0.082 2.00e-02 2.50e+03   3.73e-02 4.18e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.079 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.033 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.071 2.00e-02 2.50e+03   3.54e-02 3.77e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.060 2.00e-02 2.50e+03   2.60e-02 2.03e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 361
        2.31 -     2.88: 5212
        2.88 -     3.45: 5486
        3.45 -     4.03: 7342
        4.03 -     4.60: 10727
  Nonbonded interactions: 29128
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.748 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.782 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.798 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.804 1.730
  ... (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: 1.04
  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.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Adding C-beta torsion restraints...
  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.

        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: 100
        1.23 -     1.43: 372
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.65e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.77e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.32e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.21e+00
  bond model="   0" pdb=" CZ  ARG A  58 " segid="A   "
       model="   0" pdb=" NH2 ARG A  58 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.73e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.70 -   106.35: 136
      106.35 -   112.00: 2458
      112.00 -   117.65: 480
      117.65 -   123.30: 817
      123.30 -   128.95: 188
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.25    4.35 1.00e+00 1.00e+00 1.89e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.27    4.33 1.00e+00 1.00e+00 1.87e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.34    4.26 1.00e+00 1.00e+00 1.82e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.45    4.75 1.30e+00 5.92e-01 1.34e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.56    4.64 1.30e+00 5.92e-01 1.27e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.45: 955
       15.45 -    30.90: 55
       30.90 -    46.35: 17
       46.35 -    61.80: 3
       61.80 -    77.25: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 116 " segid="A   "
           model="   0" pdb=" C   ASP A 116 " segid="A   "
           model="   0" pdb=" N   PRO A 117 " segid="A   "
           model="   0" pdb=" CA  PRO A 117 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.00  -24.00     0      5.00e+00 4.00e-02 2.30e+01
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.10   23.90     0      5.00e+00 4.00e-02 2.29e+01
  dihedral model="   0" pdb=" CA  LEU A 119 " segid="A   "
           model="   0" pdb=" C   LEU A 119 " segid="A   "
           model="   0" pdb=" N   GLU A 120 " segid="A   "
           model="   0" pdb=" CA  GLU A 120 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.44  -17.56     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 65
       0.044 -    0.088: 53
       0.088 -    0.132: 33
       0.132 -    0.176: 22
       0.176 -    0.220: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    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  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    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 " segid="A   "    0.064 2.00e-02 2.50e+03   3.24e-02 3.14e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.020 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.068 2.00e-02 2.50e+03   2.90e-02 2.52e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03   2.74e-02 2.25e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 321
        2.30 -     2.87: 5182
        2.87 -     3.45: 5505
        3.45 -     4.02: 7304
        4.02 -     4.60: 10805
  Nonbonded interactions: 29117
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.741 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.773 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.809 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.811 1.730
  ... (remaining 29112 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: 0.82
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.89 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: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 67
        1.23 -     1.42: 405
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 8.85e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.16e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.50e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.38e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.08e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.37 -   106.11: 94
      106.11 -   111.85: 2502
      111.85 -   117.60: 483
      117.60 -   123.34: 822
      123.34 -   129.08: 178
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.97    3.63 1.00e+00 1.00e+00 1.31e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.76    4.44 1.30e+00 5.92e-01 1.17e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.78    4.42 1.30e+00 5.92e-01 1.16e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.20    3.40 1.00e+00 1.00e+00 1.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.62: 970
       14.62 -    29.24: 33
       29.24 -    43.86: 18
       43.86 -    58.48: 10
       58.48 -    73.10: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  51 " segid="A   "
           model="   0" pdb=" C   ILE A  51 " segid="A   "
           model="   0" pdb=" N   PRO A  52 " segid="A   "
           model="   0" pdb=" CA  PRO A  52 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.97   19.03     0      5.00e+00 4.00e-02 1.45e+01
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -69.99   69.99     1      3.00e+01 1.11e-03 7.02e+00
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  167.61   12.39     0      5.00e+00 4.00e-02 6.14e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.041: 78
       0.041 -    0.081: 43
       0.081 -    0.120: 37
       0.120 -    0.160: 14
       0.160 -    0.200: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    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=" CB  ILE A  77 " segid="A   "
            model="   0" pdb=" CA  ILE A  77 " segid="A   "
            model="   0" pdb=" CG1 ILE A  77 " segid="A   "
            model="   0" pdb=" CG2 ILE A  77 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.19 2.00e-01 2.50e+01 8.73e-01
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.63e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.012 2.00e-02 2.50e+03   2.83e-02 2.40e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.017 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.061 2.00e-02 2.50e+03   2.51e-02 1.89e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.052 2.00e-02 2.50e+03   2.42e-02 1.75e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.024 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 263
        2.27 -     2.85: 5064
        2.85 -     3.44: 5613
        3.44 -     4.02: 7482
        4.02 -     4.60: 11129
  Nonbonded interactions: 29551
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   SER A  46 " segid="A   "
            model="   0" pdb=" HG  SER A 130 " segid="A   "
     model   vdw
     1.691 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  47 " segid="A   "
            model="   0" pdb="HH21 ARG A 129 " segid="A   "
     model   vdw
     1.800 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.835 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.839 1.850
  nonbonded model="   0" pdb=" O   ILE A  30 " segid="A   "
            model="   0" pdb=" HG1 THR A  34 " segid="A   "
     model   vdw
     1.844 1.850
  ... (remaining 29546 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: 119
        1.23 -     1.43: 353
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.79e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.69e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.57e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.45e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.12e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.73 -   106.42: 144
      106.42 -   112.12: 2472
      112.12 -   117.81: 470
      117.81 -   123.50: 830
      123.50 -   129.20: 163
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.01    4.59 1.00e+00 1.00e+00 2.11e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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  88 " segid="A   "
        model="   0" pdb=" CB  ASP A  88 " segid="A   "
        model="   0" pdb=" CG  ASP A  88 " segid="A   "
      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 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      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 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      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 -    15.35: 964
       15.35 -    30.70: 49
       30.70 -    46.05: 14
       46.05 -    61.40: 4
       61.40 -    76.75: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.17   17.83     0      5.00e+00 4.00e-02 1.27e+01
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.95   16.05     0      5.00e+00 4.00e-02 1.03e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.30   15.70     0      5.00e+00 4.00e-02 9.87e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 61
       0.041 -    0.082: 48
       0.082 -    0.123: 42
       0.123 -    0.164: 21
       0.164 -    0.205: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    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  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 6.92e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.055 2.00e-02 2.50e+03   3.20e-02 3.08e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.022 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.041 2.00e-02 2.50e+03   2.93e-02 2.57e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.074 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.042 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.067 2.00e-02 2.50e+03   2.91e-02 2.54e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 315
        2.30 -     2.87: 5243
        2.87 -     3.45: 5606
        3.45 -     4.02: 7591
        4.02 -     4.60: 11116
  Nonbonded interactions: 29871
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.781 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.808 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.820 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.833 1.850
  ... (remaining 29866 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  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.

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.419, 47.932, 71.477, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 64
        1.23 -     1.42: 408
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  58 " segid="A   "
       model="   0" pdb=" NH2 ARG A  58 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.05e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.02e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.87e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.36e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.35e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.35 -   106.22: 103
      106.22 -   112.10: 2543
      112.10 -   117.98: 473
      117.98 -   123.86: 835
      123.86 -   129.74: 125
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A 103 " segid="A   "
        model="   0" pdb=" CB  ASP A 103 " segid="A   "
        model="   0" pdb=" CG  ASP A 103 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  108.06    4.54 1.00e+00 1.00e+00 2.06e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.29    4.31 1.00e+00 1.00e+00 1.86e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.23   -4.83 1.40e+00 5.10e-01 1.19e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.91    4.29 1.30e+00 5.92e-01 1.09e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 973
       17.69 -    35.37: 33
       35.37 -    53.06: 11
       53.06 -    70.75: 7
       70.75 -    88.43: 9
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  84 " segid="A   "
           model="   0" pdb=" CG  GLU A  84 " segid="A   "
           model="   0" pdb=" CD  GLU A  84 " segid="A   "
           model="   0" pdb=" OE1 GLU A  84 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.43  -88.43     1      3.00e+01 1.11e-03 1.04e+01
  dihedral model="   0" pdb=" CA  ASP A  88 " segid="A   "
           model="   0" pdb=" CB  ASP A  88 " segid="A   "
           model="   0" pdb=" CG  ASP A  88 " segid="A   "
           model="   0" pdb=" OD1 ASP A  88 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.46   52.46     1      2.00e+01 2.50e-03 9.38e+00
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.03  -83.03     1      3.00e+01 1.11e-03 9.37e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 78
       0.039 -    0.078: 51
       0.078 -    0.117: 28
       0.117 -    0.156: 17
       0.156 -    0.194: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  VAL A  41 " segid="A   "
            model="   0" pdb=" N   VAL A  41 " segid="A   "
            model="   0" pdb=" C   VAL A  41 " segid="A   "
            model="   0" pdb=" CB  VAL A  41 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.25    0.19 2.00e-01 2.50e+01 9.46e-01
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.41e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.75e-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 " segid="A   "   -0.098 2.00e-02 2.50e+03   4.13e-02 5.13e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.076 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.019 2.00e-02 2.50e+03   3.00e-02 2.69e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.023 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 " segid="A   "    0.052 2.00e-02 2.50e+03   2.82e-02 2.38e+01
        model="   0" pdb=" CG  TYR A  81 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 " segid="A   "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 " segid="A   "   -0.032 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.35: 635
        2.35 -     2.92: 5215
        2.92 -     3.48: 5664
        3.48 -     4.04: 7334
        4.04 -     4.60: 10863
  Nonbonded interactions: 29711
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 SER A  46 " segid="A   "
            model="   0" pdb="HG22 VAL A 126 " segid="A   "
     model   vdw
     1.793 2.440
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.803 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.818 1.850
  nonbonded model="   0" pdb=" O   GLU A  16 " segid="A   "
            model="   0" pdb=" HG1 THR A  20 " segid="A   "
     model   vdw
     1.821 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  47 " segid="A   "
            model="   0" pdb=" HZ2 LYS A 125 " segid="A   "
     model   vdw
     1.860 1.730
  ... (remaining 29706 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 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: 1.27, per 1000 atoms: 0.57
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.877, 57.579, 47.754, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.05
  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: {'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: (53.711, 44.705, 69.486, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: (53.552, 56.393, 51.466, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.07e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.01e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.85e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.74e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.57e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.04 -   105.86: 88
      105.86 -   111.68: 2425
      111.68 -   117.50: 558
      117.50 -   123.32: 822
      123.32 -   129.14: 186
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.53    4.07 1.00e+00 1.00e+00 1.66e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.19    5.01 1.30e+00 5.92e-01 1.48e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.36    4.84 1.30e+00 5.92e-01 1.38e+01
  angle model="   0" pdb=" CA  ASP A  74 " segid="A   "
        model="   0" pdb=" CB  ASP A  74 " segid="A   "
        model="   0" pdb=" CG  ASP A  74 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  108.91    3.69 1.00e+00 1.00e+00 1.36e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.37: 949
       15.37 -    30.73: 51
       30.73 -    46.10: 26
       46.10 -    61.46: 5
       61.46 -    76.83: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.22   17.78     0      5.00e+00 4.00e-02 1.26e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.05   15.95     0      5.00e+00 4.00e-02 1.02e+01
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.39    7.79     0      2.50e+00 1.60e-01 9.72e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 77
       0.051 -    0.101: 57
       0.101 -    0.152: 35
       0.152 -    0.203: 6
       0.203 -    0.253: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.73e-01
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.18 2.00e-01 2.50e+01 7.68e-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 " segid="A   "    0.208 2.00e-02 2.50e+03   9.45e-02 2.68e+02
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.192 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.109 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.088 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.098 2.00e-02 2.50e+03   3.88e-02 4.52e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.008 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.072 2.00e-02 2.50e+03   3.37e-02 3.41e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.034 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 290
        2.29 -     2.86: 5138
        2.86 -     3.44: 5505
        3.44 -     4.02: 7239
        4.02 -     4.60: 10797
  Nonbonded interactions: 28969
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.708 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.725 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.759 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.798 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.805 1.850
  ... (remaining 28964 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

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 ==============================

  Time building chain proxies: 0.70, per 1000 atoms: 0.32
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.56, 57.173, 56.556, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A 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: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 71
        1.23 -     1.42: 401
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.04e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.81e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.17e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.66e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.33 -   106.36: 136
      106.36 -   112.39: 2523
      112.39 -   118.42: 474
      118.42 -   124.45: 860
      124.45 -   130.47: 86
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.81    4.79 1.00e+00 1.00e+00 2.30e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.47   -6.07 1.40e+00 5.10e-01 1.88e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.95    5.25 1.30e+00 5.92e-01 1.63e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.07    5.13 1.30e+00 5.92e-01 1.56e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.44    4.76 1.30e+00 5.92e-01 1.34e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.43: 949
       15.43 -    30.87: 54
       30.87 -    46.30: 20
       46.30 -    61.74: 8
       61.74 -    77.17: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.61   30.39     0      5.00e+00 4.00e-02 3.69e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.65   15.35     0      5.00e+00 4.00e-02 9.43e+00
  dihedral model="   0" pdb=" N   HIS A 135 " segid="A   "
           model="   0" pdb=" CA  HIS A 135 " segid="A   "
           model="   0" pdb=" CB  HIS A 135 " segid="A   "
           model="   0" pdb=" CG  HIS A 135 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.14  -55.86     3      1.50e+01 4.44e-03 9.37e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 70
       0.047 -    0.093: 53
       0.093 -    0.139: 38
       0.139 -    0.186: 13
       0.186 -    0.232: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  THR A  83 " segid="A   "
            model="   0" pdb=" N   THR A  83 " segid="A   "
            model="   0" pdb=" C   THR A  83 " segid="A   "
            model="   0" pdb=" CB  THR A  83 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.72e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 7.84e-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 " segid="A   "    0.172 2.00e-02 2.50e+03   8.65e-02 2.24e+02
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.202 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.080 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.044 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.058 2.00e-02 2.50e+03   3.28e-02 3.23e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.068 2.00e-02 2.50e+03   3.10e-02 2.88e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.030 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 358
        2.31 -     2.88: 5231
        2.88 -     3.45: 5528
        3.45 -     4.03: 7359
        4.03 -     4.60: 10844
  Nonbonded interactions: 29320
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.733 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.770 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  40 " segid="A   "
     model   vdw
     1.823 1.730
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.824 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.834 1.850
  ... (remaining 29315 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 76
        1.23 -     1.43: 396
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.00e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.94e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.58e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.26e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.17e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.82 -   106.52: 144
      106.52 -   112.21: 2488
      112.21 -   117.91: 458
      117.91 -   123.60: 850
      123.60 -   129.30: 139
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.12    5.08 1.30e+00 5.92e-01 1.53e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.75    3.85 1.00e+00 1.00e+00 1.48e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.30   -4.90 1.40e+00 5.10e-01 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 970
       17.99 -    35.98: 41
       35.98 -    53.97: 18
       53.97 -    71.96: 1
       71.96 -    89.96: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.30   21.70     0      5.00e+00 4.00e-02 1.88e+01
  dihedral model="   0" pdb=" CA  VAL A 112 " segid="A   "
           model="   0" pdb=" C   VAL A 112 " segid="A   "
           model="   0" pdb=" N   LYS A 113 " segid="A   "
           model="   0" pdb=" CA  LYS A 113 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.91   18.09     0      5.00e+00 4.00e-02 1.31e+01
  dihedral model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
           model="   0" pdb=" CB  HIS A 139 " segid="A   "
           model="   0" pdb=" CG  HIS A 139 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -112.13   52.13     3      1.50e+01 4.44e-03 9.09e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 78
       0.047 -    0.094: 53
       0.094 -    0.140: 35
       0.140 -    0.187: 9
       0.187 -    0.234: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality model="   0" pdb=" CA  ILE A  86 " segid="A   "
            model="   0" pdb=" N   ILE A  86 " segid="A   "
            model="   0" pdb=" C   ILE A  86 " segid="A   "
            model="   0" pdb=" CB  ILE A  86 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.94e-01
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.01e-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 " segid="A   "    0.069 2.00e-02 2.50e+03   3.19e-02 3.05e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.061 2.00e-02 2.50e+03   2.72e-02 2.21e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.027 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "    0.067 2.00e-02 2.50e+03   2.55e-02 1.95e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 386
        2.32 -     2.89: 5243
        2.89 -     3.46: 5471
        3.46 -     4.03: 7341
        4.03 -     4.60: 10657
  Nonbonded interactions: 29098
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.748 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.779 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.782 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.802 1.850
  ... (remaining 29093 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: 1.06 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  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)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.757)
  Mean delta:    0.012 (Z=  0.622)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.91     4.69  1.00e+00  2.20e+01   4.7*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.18     4.42  1.00e+00  1.95e+01   4.4*sigma
   A 138  HIS  CB
   A 138  HIS  CG
   A 138  HIS  CD2       131.20   125.66     5.54  1.30e+00  1.81e+01   4.3*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.83     5.37  1.30e+00  1.71e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.056 (Z=  4.694)
  Mean delta:    1.696 (Z=  0.951)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.022
  Max. delta:   89.973
  Mean delta:   13.005

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.271
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.096
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.443
    Angle     :  1.595   7.056   4079  Z= 0.710
    Chirality :  0.082   0.271    176
    Planarity :  0.010   0.073    327
    Dihedral  : 11.264  89.973    769
    Min Nonbonded Distance : 1.757
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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: -1.52 (0.64), residues: 137
    helix: -1.82 (0.48), residues: 77
    sheet: -0.98 (1.51), residues: 10
    loop :  0.85 (0.86), residues: 50
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.007   HIS A  43 
   PHE   0.058   0.010   PHE A  67 
   TYR   0.071   0.017   TYR A  91 
   ARG   0.079   0.014   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.007   HIS A  43 
   PHE   0.041   0.011   PHE A  67 
   TYR   0.057   0.015   TYR A 111 
   ARG   0.006   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 100
        1.23 -     1.43: 372
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.53e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.20e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.77e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.49e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.48e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.39 -   106.14: 123
      106.14 -   111.89: 2449
      111.89 -   117.65: 502
      117.65 -   123.40: 830
      123.40 -   129.15: 175
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.09    4.51 1.00e+00 1.00e+00 2.04e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.15   -4.75 1.40e+00 5.10e-01 1.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.58: 948
       15.58 -    31.17: 63
       31.17 -    46.75: 17
       46.75 -    62.34: 3
       62.34 -    77.92: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 116 " segid="A   "
           model="   0" pdb=" C   ASP A 116 " segid="A   "
           model="   0" pdb=" N   PRO A 117 " segid="A   "
           model="   0" pdb=" CA  PRO A 117 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.89  -27.11     0      5.00e+00 4.00e-02 2.94e+01
  dihedral model="   0" pdb=" CA  TYR A  81 " segid="A   "
           model="   0" pdb=" C   TYR A  81 " segid="A   "
           model="   0" pdb=" N   THR A  82 " segid="A   "
           model="   0" pdb=" CA  THR A  82 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.11   25.89     0      5.00e+00 4.00e-02 2.68e+01
  dihedral model="   0" pdb=" CA  GLY A  80 " segid="A   "
           model="   0" pdb=" C   GLY A  80 " segid="A   "
           model="   0" pdb=" N   TYR A  81 " segid="A   "
           model="   0" pdb=" CA  TYR A  81 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.77   25.23     0      5.00e+00 4.00e-02 2.55e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 61
       0.047 -    0.094: 63
       0.094 -    0.140: 37
       0.140 -    0.187: 12
       0.187 -    0.233: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.154 2.00e-02 2.50e+03   8.75e-02 2.30e+02
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.196 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.090 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.120 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.041 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "    0.044 2.00e-02 2.50e+03   4.83e-02 7.00e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.117 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.084 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.019 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.057 2.00e-02 2.50e+03   3.39e-02 3.45e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.29: 320
        2.29 -     2.87: 5172
        2.87 -     3.45: 5558
        3.45 -     4.02: 7408
        4.02 -     4.60: 10942
  Nonbonded interactions: 29400
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.719 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.764 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.798 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.806 1.730
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  40 " segid="A   "
     model   vdw
     1.808 1.730
  ... (remaining 29395 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}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 76
        1.23 -     1.43: 396
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.28e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.77e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    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 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.42e+00
  bond model="   0" pdb=" CZ  ARG A  58 " segid="A   "
       model="   0" pdb=" NH2 ARG A  58 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.17e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.64 -   105.33: 55
      105.33 -   111.01: 2318
      111.01 -   116.69: 667
      116.69 -   122.38: 688
      122.38 -   128.06: 351
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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  88 " segid="A   "
        model="   0" pdb=" CB  ASP A  88 " segid="A   "
        model="   0" pdb=" CG  ASP A  88 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  108.81    3.79 1.00e+00 1.00e+00 1.44e+01
  angle model="   0" pdb=" CA  ASP A   7 " segid="A   "
        model="   0" pdb=" CB  ASP A   7 " segid="A   "
        model="   0" pdb=" CG  ASP A   7 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  108.97    3.63 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      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=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.53    4.67 1.30e+00 5.92e-01 1.29e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 967
       17.28 -    34.57: 34
       34.57 -    51.85: 17
       51.85 -    69.14: 8
       69.14 -    86.42: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" C   ILE A  77 " segid="A   "
           model="   0" pdb=" N   ILE A  77 " segid="A   "
           model="   0" pdb=" CA  ILE A  77 " segid="A   "
           model="   0" pdb=" CB  ILE A  77 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.12    9.12     0      2.50e+00 1.60e-01 1.33e+01
  dihedral model="   0" pdb=" C   HIS A 139 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
           model="   0" pdb=" CB  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.56    8.96     0      2.50e+00 1.60e-01 1.28e+01
  dihedral model="   0" pdb=" C   ASP A  44 " segid="A   "
           model="   0" pdb=" N   ASP A  44 " segid="A   "
           model="   0" pdb=" CA  ASP A  44 " segid="A   "
           model="   0" pdb=" CB  ASP A  44 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.28    8.68     0      2.50e+00 1.60e-01 1.20e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 86
       0.057 -    0.113: 53
       0.113 -    0.169: 27
       0.169 -    0.226: 7
       0.226 -    0.282: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality model="   0" pdb=" CA  HIS A 139 " segid="A   "
            model="   0" pdb=" N   HIS A 139 " segid="A   "
            model="   0" pdb=" C   HIS A 139 " segid="A   "
            model="   0" pdb=" CB  HIS A 139 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality model="   0" pdb=" CA  GLN A 100 " segid="A   "
            model="   0" pdb=" N   GLN A 100 " segid="A   "
            model="   0" pdb=" C   GLN A 100 " segid="A   "
            model="   0" pdb=" CB  GLN A 100 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.25 2.00e-01 2.50e+01 1.51e+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 " segid="A   "    0.036 2.00e-02 2.50e+03   3.38e-02 3.43e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A  43 " segid="A   "   -0.054 2.00e-02 2.50e+03   3.41e-02 2.33e+01
        model="   0" pdb=" CG  HIS A  43 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 " segid="A   "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 " segid="A   "   -0.029 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CD  ARG A 129 " segid="A   "    0.273 9.50e-02 1.11e+02   9.34e-02 1.78e+01
        model="   0" pdb=" NE  ARG A 129 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" NH1 ARG A 129 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NH2 ARG A 129 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb="HH11 ARG A 129 " segid="A   "    0.029 2.00e-02 2.50e+03
        model="   0" pdb="HH12 ARG A 129 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb="HH21 ARG A 129 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb="HH22 ARG A 129 " segid="A   "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.34: 532
        2.34 -     2.90: 5291
        2.90 -     3.47: 5613
        3.47 -     4.03: 7383
        4.03 -     4.60: 10898
  Nonbonded interactions: 29717
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A 120 " segid="A   "
            model="   0" pdb=" HZ3 LYS A 125 " segid="A   "
     model   vdw
     1.775 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.797 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.808 1.730
  nonbonded model="   0" pdb=" HZ3 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.811 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.836 1.730
  ... (remaining 29712 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}
  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.59
  MolProbity score      =   0.50

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.53, 53.441, 67.459, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 0.62, per 1000 atoms: 0.28
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.046, 48.987, 40.158, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (43.564, 76.843, 48.693, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.12 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  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: ""

  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: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 101
        1.23 -     1.43: 371
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.58e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.04e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.01e+00
  bond model="   0" pdb=" ND1 HIS A 136 " segid="A   "
       model="   0" pdb=" CE1 HIS A 136 " segid="A   "
    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=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.67e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.71 -   105.78: 86
      105.78 -   111.85: 2501
      111.85 -   117.92: 538
      117.92 -   123.99: 835
      123.99 -   130.06: 119
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A 103 " segid="A   "
        model="   0" pdb=" CB  ASP A 103 " segid="A   "
        model="   0" pdb=" CG  ASP A 103 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  107.83    4.77 1.00e+00 1.00e+00 2.28e+01
  angle model="   0" pdb=" CA  ASP A  74 " segid="A   "
        model="   0" pdb=" CB  ASP A  74 " segid="A   "
        model="   0" pdb=" CG  ASP A  74 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  107.85    4.75 1.00e+00 1.00e+00 2.26e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.20    6.00 1.30e+00 5.92e-01 2.13e+01
  angle model="   0" pdb=" CD  ARG A  58 " segid="A   "
        model="   0" pdb=" NE  ARG A  58 " segid="A   "
        model="   0" pdb=" CZ  ARG A  58 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.06   -5.66 1.40e+00 5.10e-01 1.63e+01
  angle model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
        model="   0" pdb=" NH1 ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.50  125.32   -3.82 1.00e+00 1.00e+00 1.46e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 971
       17.73 -    35.45: 27
       35.45 -    53.18: 18
       53.18 -    70.91: 8
       70.91 -    88.63: 9
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  51 " segid="A   "
           model="   0" pdb=" C   ILE A  51 " segid="A   "
           model="   0" pdb=" N   PRO A  52 " segid="A   "
           model="   0" pdb=" CA  PRO A  52 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.73   24.27     0      5.00e+00 4.00e-02 2.36e+01
  dihedral model="   0" pdb=" CB  GLU A  84 " segid="A   "
           model="   0" pdb=" CG  GLU A  84 " segid="A   "
           model="   0" pdb=" CD  GLU A  84 " segid="A   "
           model="   0" pdb=" OE1 GLU A  84 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.63   88.63     1      3.00e+01 1.11e-03 1.04e+01
  dihedral model="   0" pdb=" CB  GLU A  16 " segid="A   "
           model="   0" pdb=" CG  GLU A  16 " segid="A   "
           model="   0" pdb=" CD  GLU A  16 " segid="A   "
           model="   0" pdb=" OE1 GLU A  16 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.84   87.84     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 90
       0.057 -    0.113: 57
       0.113 -    0.169: 26
       0.169 -    0.225: 2
       0.225 -    0.282: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.47e-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 " segid="A   "    0.091 2.00e-02 2.50e+03   3.72e-02 4.16e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 136 " segid="A   "    0.050 2.00e-02 2.50e+03   2.95e-02 1.74e+01
        model="   0" pdb=" CG  HIS A 136 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 136 " segid="A   "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 136 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 136 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 136 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 136 " segid="A   "    0.020 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.011 2.00e-02 2.50e+03   2.37e-02 1.68e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.027 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 361
        2.30 -     2.88: 5202
        2.88 -     3.45: 5695
        3.45 -     4.03: 7391
        4.03 -     4.60: 11039
  Nonbonded interactions: 29688
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.730 1.730
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.815 1.850
  nonbonded model="   0" pdb=" O   ILE A  30 " segid="A   "
            model="   0" pdb=" HG1 THR A  34 " segid="A   "
     model   vdw
     1.833 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A 109 " segid="A   "
            model="   0" pdb=" OD1 ASP A 110 " segid="A   "
     model   vdw
     1.840 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.850 1.850
  ... (remaining 29683 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Adding C-beta torsion restraints...
  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.

        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: 1.04
  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.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.94 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: 67
        1.23 -     1.42: 405
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.10e+00
  bond model="   0" pdb=" CZ  ARG A 127 " segid="A   "
       model="   0" pdb=" NH2 ARG A 127 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.09e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    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=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.07e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.05e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.70 -   105.60: 84
      105.60 -   111.50: 2379
      111.50 -   117.40: 594
      117.40 -   123.30: 837
      123.30 -   129.19: 185
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.23    4.37 1.00e+00 1.00e+00 1.91e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.30    4.30 1.00e+00 1.00e+00 1.85e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      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=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.19   -4.79 1.40e+00 5.10e-01 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 960
       17.09 -    34.19: 44
       34.19 -    51.28: 24
       51.28 -    68.37: 2
       68.37 -    85.47: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 116 " segid="A   "
           model="   0" pdb=" C   ASP A 116 " segid="A   "
           model="   0" pdb=" N   PRO A 117 " segid="A   "
           model="   0" pdb=" CA  PRO A 117 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.94  -20.06     0      5.00e+00 4.00e-02 1.61e+01
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.80   19.20     0      5.00e+00 4.00e-02 1.47e+01
  dihedral model="   0" pdb=" CA  ALA A 115 " segid="A   "
           model="   0" pdb=" C   ALA A 115 " segid="A   "
           model="   0" pdb=" N   ASP A 116 " segid="A   "
           model="   0" pdb=" CA  ASP A 116 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.10   16.90     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 73
       0.047 -    0.094: 51
       0.094 -    0.142: 36
       0.142 -    0.189: 14
       0.189 -    0.236: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    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=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    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  91 " segid="A   "   -0.110 2.00e-02 2.50e+03   4.95e-02 7.34e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.091 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.044 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.081 2.00e-02 2.50e+03   3.57e-02 3.83e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.073 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.068 2.00e-02 2.50e+03   3.29e-02 3.25e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 293
        2.29 -     2.87: 5145
        2.87 -     3.45: 5574
        3.45 -     4.02: 7371
        4.02 -     4.60: 10823
  Nonbonded interactions: 29206
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.713 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.722 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.754 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  40 " segid="A   "
     model   vdw
     1.787 1.730
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.791 1.730
  ... (remaining 29201 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 53
        1.23 -     1.42: 419
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.12e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.79e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    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=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.09e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.08e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.73 -   105.57: 71
      105.57 -   111.40: 2355
      111.40 -   117.23: 627
      117.23 -   123.06: 793
      123.06 -   128.90: 233
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.88    3.72 1.00e+00 1.00e+00 1.38e+01
  angle model="   0" pdb=" CB  HIS A 136 " segid="A   "
        model="   0" pdb=" CG  HIS A 136 " segid="A   "
        model="   0" pdb=" CD2 HIS A 136 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.37    4.83 1.30e+00 5.92e-01 1.38e+01
  angle model="   0" pdb=" CA  ASN A  72 " segid="A   "
        model="   0" pdb=" CB  ASN A  72 " segid="A   "
        model="   0" pdb=" CG  ASN A  72 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.28   -3.68 1.00e+00 1.00e+00 1.35e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.62    4.58 1.30e+00 5.92e-01 1.24e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.02: 961
       16.02 -    32.03: 49
       32.03 -    48.05: 18
       48.05 -    64.06: 2
       64.06 -    80.08: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.70   31.30     0      5.00e+00 4.00e-02 3.92e+01
  dihedral model="   0" pdb=" N   HIS A 135 " segid="A   "
           model="   0" pdb=" CA  HIS A 135 " segid="A   "
           model="   0" pdb=" CB  HIS A 135 " segid="A   "
           model="   0" pdb=" CG  HIS A 135 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.51   55.51     3      1.50e+01 4.44e-03 9.35e+00
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.80   15.20     0      5.00e+00 4.00e-02 9.24e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 78
       0.053 -    0.105: 62
       0.105 -    0.158: 29
       0.158 -    0.210: 5
       0.210 -    0.263: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  89 " segid="A   "
            model="   0" pdb=" N   TYR A  89 " segid="A   "
            model="   0" pdb=" C   TYR A  89 " segid="A   "
            model="   0" pdb=" CB  TYR A  89 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.72e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.71e-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 " segid="A   "    0.066 2.00e-02 2.50e+03   3.34e-02 3.35e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.023 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.067 2.00e-02 2.50e+03   3.07e-02 2.82e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.028 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.010 2.00e-02 2.50e+03   2.82e-02 2.38e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.025 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 297
        2.28 -     2.86: 5125
        2.86 -     3.44: 5554
        3.44 -     4.02: 7347
        4.02 -     4.60: 10859
  Nonbonded interactions: 29182
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.704 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  79 " segid="A   "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.773 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.794 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.801 1.850
  ... (remaining 29177 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.83, per 1000 atoms: 0.37
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (64.385, 62.709, 46.092, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.84e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.98e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.38e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.36e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.08e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.84 -   106.49: 164
      106.49 -   112.15: 2456
      112.15 -   117.81: 464
      117.81 -   123.46: 838
      123.46 -   129.12: 157
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.21    4.39 1.00e+00 1.00e+00 1.93e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.63    4.57 1.30e+00 5.92e-01 1.23e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.12   -4.72 1.40e+00 5.10e-01 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 968
       17.79 -    35.59: 44
       35.59 -    53.38: 17
       53.38 -    71.18: 1
       71.18 -    88.97: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.40   33.60     0      5.00e+00 4.00e-02 4.52e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.32   15.68     0      5.00e+00 4.00e-02 9.83e+00
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.42   15.58     0      5.00e+00 4.00e-02 9.71e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 65
       0.048 -    0.096: 58
       0.096 -    0.144: 39
       0.144 -    0.191: 9
       0.191 -    0.239: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality model="   0" pdb=" CA  THR A  83 " segid="A   "
            model="   0" pdb=" N   THR A  83 " segid="A   "
            model="   0" pdb=" C   THR A  83 " segid="A   "
            model="   0" pdb=" CB  THR A  83 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.045 2.00e-02 2.50e+03   3.38e-02 3.43e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.088 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.046 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.071 2.00e-02 2.50e+03   3.15e-02 2.97e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.047 2.00e-02 2.50e+03   3.14e-02 2.96e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.046 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 341
        2.30 -     2.88: 5181
        2.88 -     3.45: 5470
        3.45 -     4.03: 7339
        4.03 -     4.60: 10851
  Nonbonded interactions: 29182
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.729 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.777 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.779 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.805 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.808 1.730
  ... (remaining 29177 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 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: ""
  Time building chain proxies: 0.70, per 1000 atoms: 0.32
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (75.428, 47.601, 49.894, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.09
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    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}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 51
        1.23 -     1.42: 421
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.67e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.69e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.399 -0.025 1.10e-02 8.26e+03 5.36e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.399 -0.025 1.10e-02 8.26e+03 5.35e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.04 -   106.67: 171
      106.67 -   113.30: 2616
      113.30 -   119.93: 563
      119.93 -   126.55: 712
      126.55 -   133.18: 17
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   ARG A 127 " segid="A   "
        model="   0" pdb=" N   MET A 128 " segid="A   "
        model="   0" pdb=" CA  MET A 128 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.70  133.18  -11.48 1.80e+00 3.09e-01 4.07e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.96    4.64 1.00e+00 1.00e+00 2.16e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.16    4.44 1.00e+00 1.00e+00 1.97e+01
  angle model="   0" pdb=" CA  ASP A 116 " segid="A   "
        model="   0" pdb=" CB  ASP A 116 " segid="A   "
        model="   0" pdb=" CG  ASP A 116 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  116.88   -4.28 1.00e+00 1.00e+00 1.83e+01
  angle model="   0" pdb=" C   ASP A 116 " segid="A   "
        model="   0" pdb=" CA  ASP A 116 " segid="A   "
        model="   0" pdb=" CB  ASP A 116 " segid="A   "
      ideal   model   delta    sigma   weight residual
     110.10  117.87   -7.77 1.90e+00 2.77e-01 1.67e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 957
       16.00 -    32.01: 58
       32.01 -    48.01: 14
       48.01 -    64.01: 1
       64.01 -    80.02: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 " segid="A   "
           model="   0" pdb=" C   HIS A 138 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.71   34.29     0      5.00e+00 4.00e-02 4.70e+01
  dihedral model="   0" pdb=" CA  GLU A 133 " segid="A   "
           model="   0" pdb=" C   GLU A 133 " segid="A   "
           model="   0" pdb=" N   HIS A 134 " segid="A   "
           model="   0" pdb=" CA  HIS A 134 " segid="A   "
      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  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.94   25.06     0      5.00e+00 4.00e-02 2.51e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.050: 81
       0.050 -    0.099: 48
       0.099 -    0.148: 36
       0.148 -    0.198: 7
       0.198 -    0.247: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  GLU A 133 " segid="A   "
            model="   0" pdb=" N   GLU A 133 " segid="A   "
            model="   0" pdb=" C   GLU A 133 " segid="A   "
            model="   0" pdb=" CB  GLU A 133 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality model="   0" pdb=" CA  ILE A 122 " segid="A   "
            model="   0" pdb=" N   ILE A 122 " segid="A   "
            model="   0" pdb=" C   ILE A 122 " segid="A   "
            model="   0" pdb=" CB  ILE A 122 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    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  68 " segid="A   "   -0.048 2.00e-02 2.50e+03   3.44e-02 3.55e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.085 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.052 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.062 2.00e-02 2.50e+03   3.12e-02 2.93e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.061 2.00e-02 2.50e+03   2.66e-02 2.12e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.28: 301
        2.28 -     2.86: 5119
        2.86 -     3.44: 5473
        3.44 -     4.02: 7218
        4.02 -     4.60: 10573
  Nonbonded interactions: 28684
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.705 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.779 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.803 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.810 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.815 1.730
  ... (remaining 28679 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.04, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.825, 71.841, 57.384, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 66
        1.23 -     1.42: 406
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.77e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.51e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.19e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.81e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.66e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.29 -   106.09: 110
      106.09 -   111.89: 2464
      111.89 -   117.69: 500
      117.69 -   123.49: 846
      123.49 -   129.29: 159
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.79    4.81 1.00e+00 1.00e+00 2.31e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.96    5.24 1.30e+00 5.92e-01 1.62e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.29   -4.89 1.40e+00 5.10e-01 1.22e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.13    3.47 1.00e+00 1.00e+00 1.20e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.51: 949
       15.51 -    31.02: 56
       31.02 -    46.53: 21
       46.53 -    62.04: 5
       62.04 -    77.55: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 " segid="A   "
           model="   0" pdb=" C   ASP A 118 " segid="A   "
           model="   0" pdb=" N   LEU A 119 " segid="A   "
           model="   0" pdb=" CA  LEU A 119 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.77   35.23     0      5.00e+00 4.00e-02 4.97e+01
  dihedral model="   0" pdb=" CA  LEU A 132 " segid="A   "
           model="   0" pdb=" C   LEU A 132 " segid="A   "
           model="   0" pdb=" N   GLU A 133 " segid="A   "
           model="   0" pdb=" CA  GLU A 133 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.74   25.26     0      5.00e+00 4.00e-02 2.55e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.09   21.91     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 68
       0.046 -    0.091: 55
       0.091 -    0.136: 36
       0.136 -    0.182: 13
       0.182 -    0.227: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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=" CB  ILE A  77 " segid="A   "
            model="   0" pdb=" CA  ILE A  77 " segid="A   "
            model="   0" pdb=" CG1 ILE A  77 " segid="A   "
            model="   0" pdb=" CG2 ILE A  77 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.92e-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 " segid="A   "    0.059 2.00e-02 2.50e+03   3.17e-02 3.01e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 " segid="A   "    0.065 2.00e-02 2.50e+03   3.82e-02 2.91e+01
        model="   0" pdb=" CG  HIS A 139 " segid="A   "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 " segid="A   "   -0.049 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 " segid="A   "    0.031 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.056 2.00e-02 2.50e+03   2.50e-02 1.88e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.024 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 290
        2.28 -     2.86: 5130
        2.86 -     3.44: 5484
        3.44 -     4.02: 7251
        4.02 -     4.60: 10768
  Nonbonded interactions: 28923
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.699 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.722 1.850
  nonbonded model="   0" pdb="HG12 ILE A  77 " segid="A   "
            model="   0" pdb="HG21 THR A  82 " segid="A   "
     model   vdw
     1.793 2.440
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.814 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.821 1.730
  ... (remaining 28918 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 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: 1.03
  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}

============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 62
        1.23 -     1.42: 410
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.39e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    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=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.44e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.13e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.86e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.82 -   105.71: 87
      105.71 -   111.60: 2406
      111.60 -   117.49: 571
      117.49 -   123.38: 843
      123.38 -   129.27: 172
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.13    4.47 1.00e+00 1.00e+00 2.00e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.15    5.05 1.30e+00 5.92e-01 1.51e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.27   -4.87 1.40e+00 5.10e-01 1.21e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.70: 954
       15.70 -    31.39: 56
       31.39 -    47.09: 17
       47.09 -    62.79: 4
       62.79 -    78.48: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 135 " segid="A   "
           model="   0" pdb=" C   HIS A 135 " segid="A   "
           model="   0" pdb=" N   HIS A 136 " segid="A   "
           model="   0" pdb=" CA  HIS A 136 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.13   26.87     0      5.00e+00 4.00e-02 2.89e+01
  dihedral model="   0" pdb=" CA  HIS A 138 " segid="A   "
           model="   0" pdb=" C   HIS A 138 " segid="A   "
           model="   0" pdb=" N   HIS A 139 " segid="A   "
           model="   0" pdb=" CA  HIS A 139 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.55   24.45     0      5.00e+00 4.00e-02 2.39e+01
  dihedral model="   0" pdb=" CA  HIS A 137 " segid="A   "
           model="   0" pdb=" C   HIS A 137 " segid="A   "
           model="   0" pdb=" N   HIS A 138 " segid="A   "
           model="   0" pdb=" CA  HIS A 138 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.08   20.92     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 75
       0.052 -    0.104: 55
       0.104 -    0.155: 33
       0.155 -    0.207: 10
       0.207 -    0.259: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 " segid="A   "
            model="   0" pdb=" N   LYS A  85 " segid="A   "
            model="   0" pdb=" C   LYS A  85 " segid="A   "
            model="   0" pdb=" CB  LYS A  85 " segid="A   "
    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  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality model="   0" pdb=" CA  HIS A 135 " segid="A   "
            model="   0" pdb=" N   HIS A 135 " segid="A   "
            model="   0" pdb=" C   HIS A 135 " segid="A   "
            model="   0" pdb=" CB  HIS A 135 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+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 " segid="A   "   -0.085 2.00e-02 2.50e+03   3.65e-02 4.00e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "    0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "    0.027 2.00e-02 2.50e+03   3.25e-02 3.17e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "   -0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "    0.069 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "   -0.022 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.069 2.00e-02 2.50e+03   3.12e-02 2.93e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.064 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.030 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 249
        2.27 -     2.86: 5063
        2.86 -     3.44: 5597
        3.44 -     4.02: 7310
        4.02 -     4.60: 10862
  Nonbonded interactions: 29081
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.693 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.734 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.782 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.793 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.814 1.730
  ... (remaining 29076 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 56
        1.23 -     1.42: 416
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.405 -0.031 1.10e-02 8.26e+03 7.69e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.89e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.49e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.35e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.68e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.32 -   106.44: 136
      106.44 -   112.56: 2541
      112.56 -   118.68: 487
      118.68 -   124.79: 849
      124.79 -   130.91: 66
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.78    4.82 1.00e+00 1.00e+00 2.32e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.91   -6.51 1.40e+00 5.10e-01 2.16e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.03    4.57 1.00e+00 1.00e+00 2.08e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.16    5.04 1.30e+00 5.92e-01 1.50e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.74: 952
       15.74 -    31.47: 60
       31.47 -    47.21: 14
       47.21 -    62.94: 5
       62.94 -    78.68: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.79   24.21     0      5.00e+00 4.00e-02 2.35e+01
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.25   20.75     0      5.00e+00 4.00e-02 1.72e+01
  dihedral model="   0" pdb=" CA  LYS A 113 " segid="A   "
           model="   0" pdb=" C   LYS A 113 " segid="A   "
           model="   0" pdb=" N   PRO A 114 " segid="A   "
           model="   0" pdb=" CA  PRO A 114 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.18   16.82     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 74
       0.045 -    0.089: 50
       0.089 -    0.133: 31
       0.133 -    0.178: 19
       0.178 -    0.222: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.98e-01
  chirality model="   0" pdb=" CA  ILE A  86 " segid="A   "
            model="   0" pdb=" N   ILE A  86 " segid="A   "
            model="   0" pdb=" C   ILE A  86 " segid="A   "
            model="   0" pdb=" CB  ILE A  86 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.47e-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 " segid="A   "   -0.065 2.00e-02 2.50e+03   3.16e-02 3.00e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.015 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.036 2.00e-02 2.50e+03   2.90e-02 2.53e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.076 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.038 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane m        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
odel="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.065 2.00e-02 2.50e+03   2.84e-02 2.43e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.022 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.31: 378
        2.31 -     2.88: 5247
        2.88 -     3.45: 5580
        3.45 -     4.03: 7557
        4.03 -     4.60: 11126
  Nonbonded interactions: 29888
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.737 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.768 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  40 " segid="A   "
     model   vdw
     1.794 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.810 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  49 " segid="A   "
            model="   0" pdb=" HZ1 LYS A 113 " segid="A   "
     model   vdw
     1.820 1.730
  ... (remaining 29883 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: ""
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (58.815, 49.381, 48.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 1.09 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.256, 54.995, 76.501, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 66
        1.23 -     1.42: 406
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.89e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.70e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.57e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.52e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.42e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.81 -   106.66: 166
      106.66 -   112.50: 2522
      112.50 -   118.35: 438
      118.35 -   124.20: 857
      124.20 -   130.04: 96
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.93    4.67 1.00e+00 1.00e+00 2.18e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.04   -5.64 1.40e+00 5.10e-01 1.62e+01
  angle model="   0" pdb=" C   LYS A  85 " segid="A   "
        model="   0" pdb=" N   ILE A  86 " segid="A   "
        model="   0" pdb=" CA  ILE A  86 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.70  128.45   -6.75 1.80e+00 3.09e-01 1.41e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      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 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.65    4.55 1.30e+00 5.92e-01 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 962
       16.01 -    32.02: 50
       32.02 -    48.03: 17
       48.03 -    64.03: 1
       64.03 -    80.04: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  87 " segid="A   "
           model="   0" pdb=" C   GLY A  87 " segid="A   "
           model="   0" pdb=" N   ASP A  88 " segid="A   "
           model="   0" pdb=" CA  ASP A  88 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.46  -24.54     0      5.00e+00 4.00e-02 2.41e+01
  dihedral model="   0" pdb=" CA  GLU A  84 " segid="A   "
           model="   0" pdb=" C   GLU A  84 " segid="A   "
           model="   0" pdb=" N   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.10   15.90     0      5.00e+00 4.00e-02 1.01e+01
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.54   15.46     0      5.00e+00 4.00e-02 9.56e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 77
       0.046 -    0.093: 50
       0.093 -    0.139: 33
       0.139 -    0.186: 14
       0.186 -    0.232: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.19 2.00e-01 2.50e+01 8.71e-01
  chirality model="   0" pdb=" CB  ILE A  77 " segid="A   "
            model="   0" pdb=" CA  ILE A  77 " segid="A   "
            model="   0" pdb=" CG1 ILE A  77 " segid="A   "
            model="   0" pdb=" CG2 ILE A  77 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 7.93e-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 " segid="A   "   -0.044 2.00e-02 2.50e+03   3.03e-02 2.75e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.074 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.045 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 " segid="A   "    0.059 2.00e-02 2.50e+03   3.55e-02 2.53e+01
        model="   0" pdb=" CG  HIS A 139 " segid="A   "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 " segid="A   "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 " segid="A   "    0.032 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03   2.75e-02 2.26e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.029 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 290
        2.28 -     2.86: 5105
        2.86 -     3.44: 5528
        3.44 -     4.02: 7330
        4.02 -     4.60: 10760
  Nonbonded interactions: 29013
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.705 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.758 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.766 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.773 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.808 1.850
  ... (remaining 29008 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: 0.63
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.70 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 71
        1.23 -     1.43: 401
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 7.18e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.70e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.46e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.31e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.13e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.84 -   106.53: 154
      106.53 -   112.21: 2477
      112.21 -   117.89: 458
      117.89 -   123.57: 843
      123.57 -   129.26: 147
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.90    4.70 1.00e+00 1.00e+00 2.21e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.26   -4.86 1.40e+00 5.10e-01 1.20e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.15    3.45 1.00e+00 1.00e+00 1.19e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 970
       18.00 -    35.99: 47
       35.99 -    53.98: 12
       53.98 -    71.98: 1
       71.98 -    89.97: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.46   20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral model="   0" pdb=" CA  PRO A 102 " segid="A   "
           model="   0" pdb=" C   PRO A 102 " segid="A   "
           model="   0" pdb=" N   ASP A 103 " segid="A   "
           model="   0" pdb=" CA  ASP A 103 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.26   14.74     0      5.00e+00 4.00e-02 8.69e+00
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.63   78.63     1      3.00e+01 1.11e-03 8.56e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.048: 76
       0.048 -    0.094: 51
       0.094 -    0.140: 35
       0.140 -    0.186: 13
       0.186 -    0.232: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.24e-01
  chirality model="   0" pdb=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.64e-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 " segid="A   "    0.060 2.00e-02 2.50e+03   3.98e-02 4.76e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.099 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "   -0.055 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.060 2.00e-02 2.50e+03   3.05e-02 2.80e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "   -0.059 2.00e-02 2.50e+03   2.65e-02 2.11e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.024 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 354
        2.31 -     2.88: 5181
        2.88 -     3.45: 5456
        3.45 -     4.03: 7234
        4.03 -     4.60: 10562
  Nonbonded interactions: 28787
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.733 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.778 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.804 1.730
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.814 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.822 1.850
  ... (remaining 28782 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: 0.60
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.68 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  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=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.43e+00
  bond model="   0" pdb=" CE1 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.96e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.96e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.92e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.52 -   106.49: 150
      106.49 -   112.45: 2521
      112.45 -   118.42: 476
      118.42 -   124.39: 831
      124.39 -   130.36: 101
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   GLU A 133 " segid="A   "
        model="   0" pdb=" N   HIS A 134 " segid="A   "
        model="   0" pdb=" CA  HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.70  130.36   -8.66 1.80e+00 3.09e-01 2.32e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.91    4.69 1.00e+00 1.00e+00 2.20e+01
  angle model="   0" pdb=" CB  HIS A 134 " segid="A   "
        model="   0" pdb=" CG  HIS A 134 " segid="A   "
        model="   0" pdb=" CD2 HIS A 134 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  125.27    5.93 1.30e+00 5.92e-01 2.08e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.38    4.22 1.00e+00 1.00e+00 1.78e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 950
       16.01 -    32.02: 50
       32.02 -    48.03: 25
       48.03 -    64.03: 5
       64.03 -    80.04: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 116 " segid="A   "
           model="   0" pdb=" C   ASP A 116 " segid="A   "
           model="   0" pdb=" N   PRO A 117 " segid="A   "
           model="   0" pdb=" CA  PRO A 117 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.85  -20.15     0      5.00e+00 4.00e-02 1.62e+01
  dihedral model="   0" pdb=" C   HIS A 135 " segid="A   "
           model="   0" pdb=" N   HIS A 135 " segid="A   "
           model="   0" pdb=" CA  HIS A 135 " segid="A   "
           model="   0" pdb=" CB  HIS A 135 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.12    9.52     0      2.50e+00 1.60e-01 1.45e+01
  dihedral model="   0" pdb=" CA  HIS A 135 " segid="A   "
           model="   0" pdb=" C   HIS A 135 " segid="A   "
           model="   0" pdb=" N   HIS A 136 " segid="A   "
           model="   0" pdb=" CA  HIS A 136 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.93   18.07     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 81
       0.059 -    0.117: 62
       0.117 -    0.175: 30
       0.175 -    0.234: 1
       0.234 -    0.292: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 135 " segid="A   "
            model="   0" pdb=" N   HIS A 135 " segid="A   "
            model="   0" pdb=" C   HIS A 135 " segid="A   "
            model="   0" pdb=" CB  HIS A 135 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality model="   0" pdb=" CA  ASP A  44 " segid="A   "
            model="   0" pdb=" N   ASP A  44 " segid="A   "
            model="   0" pdb=" C   ASP A  44 " segid="A   "
            model="   0" pdb=" CB  ASP A  44 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.082 2.00e-02 2.50e+03   3.67e-02 4.04e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.075 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.031 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03   3.33e-02 3.33e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.053 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.013 2.00e-02 2.50e+03   2.94e-02 2.60e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.038 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 315
        2.29 -     2.87: 5136
        2.87 -     3.44: 5401
        3.44 -     4.02: 7213
        4.02 -     4.60: 10653
  Nonbonded interactions: 28718
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.712 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.800 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.825 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.828 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  27 " segid="A   "
     model   vdw
     1.829 1.730
  ... (remaining 28713 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}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.913, 41.033, 61.525, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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=  2.731)
  Mean delta:    0.013 (Z=  0.659)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.86     4.74  1.00e+00  2.25e+01   4.7*sigma
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   129.00    -7.30  1.80e+00  1.65e+01   4.1*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.59     4.01  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.937 (Z=  4.739)
  Mean delta:    1.794 (Z=  0.985)

                      ----------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   155.73    24.27  5.00e+00  2.36e+01   4.9*sigma

  Min. delta:    0.010
  Max. delta:   76.312
  Mean delta:   12.974

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.237
  Mean delta:    0.082

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.059       0.102       69.35   5.1*sigma

  Min. delta:    0.000
  Max. delta:    0.104
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.661   7.937   4079  Z= 0.733
    Chirality :  0.082   0.237    176
    Planarity :  0.011   0.079    327
    Dihedral  : 11.602  80.025    769
    Min Nonbonded Distance : 1.727
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  4.03 %
      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: -1.21 (0.68), residues: 137
    helix: -1.05 (0.45), residues: 92
    sheet: -2.05 (1.38), residues: 10
    loop :  1.08 (1.26), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.043   0.009   PHE A  67 
   TYR   0.123   0.019   TYR A  91 
   ARG   0.086   0.023   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.030   0.008   PHE A  67 
   TYR   0.102   0.023   TYR A  91 
   ARG   0.009   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   0.82

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=  2.733)
  Mean delta:    0.013 (Z=  0.661)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.30     4.30  1.00e+00  1.85e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.546 (Z=  4.304)
  Mean delta:    1.815 (Z=  0.997)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.016
  Max. delta:   76.053
  Mean delta:   12.718

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.238
  Mean delta:    0.086

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  12  TYR  CB
   A  12  TYR  CG
   A  12  TYR  CD1
   A  12  TYR  CD2
   A  12  TYR  CE1
   A  12  TYR  CE2
   A  12  TYR  CZ
   A  12  TYR  OH            0.045       0.080       41.19   4.0*sigma

  Min. delta:    0.000
  Max. delta:    0.082
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.471
    Angle     :  1.680   7.546   4079  Z= 0.742
    Chirality :  0.086   0.238    176
    Planarity :  0.010   0.062    327
    Dihedral  : 11.938  76.053    769
    Min Nonbonded Distance : 1.694
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.57 (0.72), residues: 137
    helix: -2.14 (0.47), residues: 78
    sheet: -0.89 (1.71), residues: 10
    loop :  1.43 (1.06), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A  43 
   PHE   0.066   0.011   PHE A  67 
   TYR   0.095   0.015   TYR A  12 
   ARG   0.069   0.016   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.004   HIS A  43 
   PHE   0.046   0.010   PHE A  67 
   TYR   0.080   0.016   TYR A  12 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.68
  MolProbity score      =   0.90

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=  2.624)
  Mean delta:    0.013 (Z=  0.670)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   117.89    -5.29  1.00e+00  2.80e+01   5.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.77     4.83  1.00e+00  2.33e+01   4.8*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.08     4.52  1.00e+00  2.05e+01   4.5*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.79     5.41  1.30e+00  1.73e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.101 (Z=  5.295)
  Mean delta:    1.840 (Z=  1.030)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.019
  Max. delta:   81.134
  Mean delta:   13.505

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.249
  Mean delta:    0.084

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.086
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.477
    Angle     :  1.685   8.101   4079  Z= 0.758
    Chirality :  0.084   0.249    176
    Planarity :  0.010   0.065    327
    Dihedral  : 11.800  81.134    769
    Min Nonbonded Distance : 1.728
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.92 %
      Favored  : 96.35 %
    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: -1.58 (0.66), residues: 137
    helix: -1.32 (0.46), residues: 87
    sheet: -2.16 (1.49), residues: 10
    loop :  0.55 (1.10), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.046   0.008   PHE A  67 
   TYR   0.086   0.014   TYR A 111 
   ARG   0.070   0.015   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.031   0.008   PHE A  67 
   TYR   0.075   0.015   TYR A 111 
   ARG   0.005   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  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.

  Ramachandran outliers =   0.73 %
                favored =  96.35 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.68
  MolProbity score      =   1.19

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: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 83
        1.23 -     1.43: 389
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.50e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.49e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.30e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.27e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.20e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.30 -   107.13: 410
      107.13 -   112.96: 2339
      112.96 -   118.79: 434
      118.79 -   124.62: 805
      124.62 -   130.45: 91
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 " segid="A   "
        model="   0" pdb=" N   ILE A  86 " segid="A   "
        model="   0" pdb=" CA  ILE A  86 " segid="A   "
      ideal   model   delta    sigma   weight residual
     121.70  130.45   -8.75 1.80e+00 3.09e-01 2.37e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.92    4.68 1.00e+00 1.00e+00 2.19e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      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  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.23   -4.83 1.40e+00 5.10e-01 1.19e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 950
       16.01 -    32.01: 54
       32.01 -    48.02: 23
       48.02 -    64.02: 3
       64.02 -    80.03: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.63   26.37     0      5.00e+00 4.00e-02 2.78e+01
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.54   21.46     0      5.00e+00 4.00e-02 1.84e+01
  dihedral model="   0" pdb=" C   ILE A  71 " segid="A   "
           model="   0" pdb=" N   ILE A  71 " segid="A   "
           model="   0" pdb=" CA  ILE A  71 " segid="A   "
           model="   0" pdb=" CB  ILE A  71 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -129.60    7.60     0      2.50e+00 1.60e-01 9.23e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 77
       0.050 -    0.099: 56
       0.099 -    0.149: 33
       0.149 -    0.199: 9
       0.199 -    0.248: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality model="   0" pdb=" CA  HIS A 138 " segid="A   "
            model="   0" pdb=" N   HIS A 138 " segid="A   "
            model="   0" pdb=" C   HIS A 138 " segid="A   "
            model="   0" pdb=" CB  HIS A 138 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.92e-01
  chirality model="   0" pdb=" CB  ILE A  77 " segid="A   "
            model="   0" pdb=" CA  ILE A  77 " segid="A   "
            model="   0" pdb=" CG1 ILE A  77 " segid="A   "
            model="   0" pdb=" CG2 ILE A  77 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.17 2.00e-01 2.50e+01 7.07e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.074 2.00e-02 2.50e+03   3.23e-02 3.13e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.012 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "    0.044 2.00e-02 2.50e+03   3.16e-02 3.00e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "    0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.001 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 " segid="A   "    0.065 2.00e-02 2.50e+03   2.74e-02 2.26e+01
        model="   0" pdb=" CG  TYR A  50 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 " segid="A   "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 " segid="A   "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 " segid="A   "   -0.025 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 292
        2.28 -     2.86: 5118
        2.86 -     3.44: 5547
        3.44 -     4.02: 7357
        4.02 -     4.60: 10821
  Nonbonded interactions: 29135
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ2 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.702 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.707 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.780 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.790 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.796 1.850
  ... (remaining 29130 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: 0.89
  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.


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=  2.703)
  Mean delta:    0.013 (Z=  0.647)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.92     4.68  1.00e+00  2.19e+01   4.7*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.803 (Z=  4.676)
  Mean delta:    1.872 (Z=  0.999)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   136.61    43.39  5.00e+00  7.53e+01   8.7*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   146.24    33.76  5.00e+00  4.56e+01   6.8*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   153.35    26.65  5.00e+00  2.84e+01   5.3*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   153.73    26.27  5.00e+00  2.76e+01   5.3*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   154.18    25.82  5.00e+00  2.67e+01   5.2*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   155.72    24.28  5.00e+00  2.36e+01   4.9*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   155.97    24.03  5.00e+00  2.31e+01   4.8*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   156.23    23.77  5.00e+00  2.26e+01   4.8*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   156.69    23.31  5.00e+00  2.17e+01   4.7*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   156.79    23.21  5.00e+00  2.15e+01   4.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   159.68    20.32  5.00e+00  1.65e+01   4.1*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00   159.81    20.19  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.003
  Max. delta:   76.740
  Mean delta:   13.022

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.249
  Mean delta:    0.085

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.105
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 65
        1.23 -     1.42: 407
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.72e+00
  bond model="   0" pdb=" CZ  ARG A  58 " segid="A   "
       model="   0" pdb=" NH2 ARG A  58 " segid="A   "
    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=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.399 -0.025 1.10e-02 8.26e+03 5.16e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.399 -0.025 1.10e-02 8.26e+03 5.11e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.399 -0.025 1.10e-02 8.26e+03 5.10e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.82 -   105.65: 69
      105.65 -   111.49: 2407
      111.49 -   117.32: 597
      117.32 -   123.15: 795
      123.15 -   128.98: 211
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CB  HIS A 137 " segid="A   "
        model="   0" pdb=" CG  HIS A 137 " segid="A   "
        model="   0" pdb=" CD2 HIS A 137 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.43    4.77 1.30e+00 5.92e-01 1.34e+01
  angle model="   0" pdb=" CB  HIS A  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      ideal   model   delta    sigma   weight residual
     131.20  126.84    4.36 1.30e+00 5.92e-01 1.12e+01
  angle model="   0" pdb=" CB  HIS A 135 " segid="A   "
        model="   0" pdb=" CG  HIS A 135 " segid="A   "
        model="   0" pdb=" CD2 HIS A 135 " segid="A   "
      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=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  119.29    3.31 1.00e+00 1.00e+00 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.34: 972
       16.34 -    32.68: 36
       32.68 -    49.01: 18
       49.01 -    65.35: 3
       65.35 -    81.69: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  84 " segid="A   "
           model="   0" pdb=" CG  GLU A  84 " segid="A   "
           model="   0" pdb=" CD  GLU A  84 " segid="A   "
           model="   0" pdb=" OE1 GLU A  84 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.69  -81.69     1      3.00e+01 1.11e-03 9.13e+00
  dihedral model="   0" pdb=" CB  GLU A   8 " segid="A   "
           model="   0" pdb=" CG  GLU A   8 " segid="A   "
           model="   0" pdb=" CD  GLU A   8 " segid="A   "
           model="   0" pdb=" OE1 GLU A   8 " segid="A   "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.24  -81.24     1      3.00e+01 1.11e-03 9.04e+00
  dihedral model="   0" pdb=" C   LYS A  85 " segid="A   "
           model="   0" pdb=" N  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.461
    Angle     :  1.702   8.803   4079  Z= 0.743
    Chirality :  0.085   0.249    176
    Planarity :  0.011   0.080    327
    Dihedral  : 11.869  76.740    769
    Min Nonbonded Distance : 1.716
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  7.30 %
      Allowed  :  7.30 %
      Favored  : 85.40 %
    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 : 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: -3.29 (0.63), residues: 137
    helix: -1.85 (0.48), residues: 70
    sheet: -2.15 (1.40), residues: 10
    loop : -2.49 (0.85), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.046   0.009   PHE A  67 
   TYR   0.092   0.019   TYR A  68 
   ARG   0.088   0.016   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.031   0.008   PHE A  67 
   TYR   0.070   0.019   TYR A  68 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

   LYS A  85 " segid="A   "
           model="   0" pdb=" CA  LYS A  85 " segid="A   "
           model="   0" pdb=" CB  LYS A  85 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.09    7.49     0      2.50e+00 1.60e-01 8.99e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.045: 72
       0.045 -    0.089: 53
       0.089 -    0.132: 33
       0.132 -    0.176: 13
       0.176 -    0.220: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 " segid="A   "
            model="   0" pdb=" N   LYS A  85 " segid="A   "
            model="   0" pdb=" C   LYS A  85 " segid="A   "
            model="   0" pdb=" CB  LYS A  85 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.20 2.00e-01 2.50e+01 9.51e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.30e-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 " segid="A   "    0.028 2.00e-02 2.50e+03   3.04e-02 2.76e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.040 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A  43 " segid="A   "    0.054 2.00e-02 2.50e+03   3.32e-02 2.20e+01
        model="   0" pdb=" CG  HIS A  43 " segid="A   "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A  43 " segid="A   "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A  43 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A  43 " segid="A   "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A  43 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A  43 " segid="A   "    0.028 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.049 2.00e-02 2.50e+03   2.27e-02 1.54e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.37: 733
        2.37 -     2.93: 5124
        2.93 -     3.48: 5396
        3.48 -     4.04: 7095
        4.04 -     4.60: 10386
  Nonbonded interactions: 28734
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.808 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.819 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.831 1.850
  nonbonded model="   0" pdb=" O   GLU A  16 " segid="A   "
            model="   0" pdb=" HG1 THR A  20 " segid="A   "
     model   vdw
     1.833 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 " segid="A   "
            model="   0" pdb=" HG  SER A  65 " segid="A   "
     model   vdw
     1.833 1.850
  ... (remaining 28729 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   7.30 %
                favored =  85.40 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0090
  RMS(angles)           =   1.70
  MolProbity score      =   1.43

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: 0.94
  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.

  Time building chain proxies: 0.74, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.255, 69.599, 51.679, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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: 55
        1.23 -     1.42: 417
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.72e+00
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.59e+00
  bond model="   0" pdb=" CD2 HIS A 136 " segid="A   "
       model="   0" pdb=" NE2 HIS A 136 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.92e+00
  bond model="   0" pdb=" CD2 HIS A 134 " segid="A   "
       model="   0" pdb=" NE2 HIS A 134 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 5.85e+00
  bond model="   0" pdb=" CE1 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.79e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       98.84 -   104.88: 42
      104.88 -   110.92: 2287
      110.92 -   116.96: 712
      116.96 -   123.01: 791
      123.01 -   129.05: 247
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.24    4.36 1.00e+00 1.00e+00 1.90e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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=" CG  LYS A  19 " segid="A   "
        model="   0" pdb=" CD  LYS A  19 " segid="A   "
        model="   0" pdb=" CE  LYS A  19 " segid="A   "
      ideal   model   delta    sigma   weight residual
     111.30  103.26    8.04 2.30e+00 1.89e-01 1.22e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.05   -4.65 1.40e+00 5.10e-01 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 960
       16.01 -    32.01: 51
       32.01 -    48.02: 15
       48.02 -    64.03: 4
       64.03 -    80.03: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" C   SER A  98 " segid="A   "
           model="   0" pdb=" N   SER A  98 " segid="A   "
           model="   0" pdb=" CA  SER A  98 " segid="A   "
           model="   0" pdb=" CB  SER A  98 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.17    8.57     0      2.50e+00 1.60e-01 1.18e+01
  dihedral model="   0" pdb=" CA  TYR A  81 " segid="A   "
           model="   0" pdb=" C   TYR A  81 " segid="A   "
           model="   0" pdb=" N   THR A  82 " segid="A   "
           model="   0" pdb=" CA  THR A  82 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.88   16.12     0      5.00e+00 4.00e-02 1.04e+01
  dihedral model="   0" pdb=" C   PHE A  45 " segid="A   "
           model="   0" pdb=" N   PHE A  45 " segid="A   "
           model="   0" pdb=" CA  PHE A  45 " segid="A   "
           model="   0" pdb=" CB  PHE A  45 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.45    7.85     0      2.50e+00 1.60e-01 9.86e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 96
       0.064 -    0.127: 57
       0.127 -    0.190: 21
       0.190 -    0.254: 1
       0.254 -    0.317: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  98 " segid="A   "
            model="   0" pdb=" N   SER A  98 " segid="A   "
            model="   0" pdb=" C   SER A  98 " segid="A   "
            model="   0" pdb=" CB  SER A  98 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.51e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    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  12 " segid="A   "   -0.075 2.00e-02 2.50e+03   3.34e-02 3.35e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "   -0.069 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "    0.029 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "    0.062 2.00e-02 2.50e+03   3.18e-02 3.03e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.017 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.046 2.00e-02 2.50e+03   3.07e-02 2.82e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 280
        2.28 -     2.86: 5122
        2.86 -     3.44: 5622
        3.44 -     4.02: 7408
        4.02 -     4.60: 11092
  Nonbonded interactions: 29524
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.703 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" O   ASP A 118 " segid="A   "
            model="   0" pdb=" HZ2 LYS A 125 " segid="A   "
     model   vdw
     1.771 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.787 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  40 " segid="A   "
     model   vdw
     1.816 1.730
  ... (remaining 29519 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.038 (Z=  2.666)
  Mean delta:    0.013 (Z=  0.665)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.66    -6.26  1.40e+00  2.00e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.33     4.27  1.00e+00  1.82e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.877 (Z=  4.472)
  Mean delta:    1.798 (Z=  0.995)

                      ----------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   158.98    21.02  5.00e+00  1.77e+01   4.2*sigma
   A 121  GLY  CA
   A 121  GLY  C
   A 122  ILE  N
   A 122  ILE  CA        180.00  -159.67   -20.33  5.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.007
  Max. delta:   77.844
  Mean delta:   13.531

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.225
  Mean delta:    0.085

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.077
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.474
    Angle     :  1.675   7.877   4079  Z= 0.742
    Chirality :  0.085   0.225    176
    Planarity :  0.009   0.060    327
    Dihedral  : 11.946  77.844    769
    Min Nonbonded Distance : 1.716
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    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: -1.86 (0.66), residues: 137
    helix: -1.87 (0.45), residues: 83
    sheet: -1.35 (1.69), residues: 10
    loop :  0.72 (1.00), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.041   0.009   PHE A  67 
   TYR   0.076   0.015   TYR A 111 
   ARG   0.067   0.014   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.028   0.007   PHE A  67 
   TYR   0.068   0.015   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 =  94.89 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.67
  MolProbity score      =   1.28

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:    0.043 (Z=  2.826)
  Mean delta:    0.012 (Z=  0.631)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.29     5.91  1.30e+00  2.07e+01   4.5*sigma
   A 139  HIS  CB
   A 139  HIS  CG
   A 139  HIS  CD2       131.20   125.56     5.64  1.30e+00  1.88e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.39     4.21  1.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.805 (Z=  4.549)
  Mean delta:    1.718 (Z=  0.958)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   82.131
  Mean delta:   10.122

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.233
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.072
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.043   2242  Z= 0.450
    Angle     :  1.612   7.805   4079  Z= 0.715
    Chirality :  0.082   0.233    176
    Planarity :  0.010   0.055    327
    Dihedral  :  9.811  82.131    769
    Min Nonbonded Distance : 1.763
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  3.65 %
      Favored  : 94.89 %
    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: -1.94 (0.64), residues: 137
    helix: -1.19 (0.52), residues: 70
    sheet: -1.33 (1.34), residues: 10
    loop : -1.19 (0.83), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.034   0.009   HIS A 138 
   PHE   0.049   0.009   PHE A  67 
   TYR   0.078   0.014   TYR A  91 
   ARG   0.058   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.034   0.009   HIS A 138 
   PHE   0.035   0.008   PHE A  67 
   TYR   0.052   0.014   TYR A 111 
   ARG   0.009   0.003   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  94.89 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0088
  RMS(angles)           =   1.61
  MolProbity score      =   1.13

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:    0.037 (Z=  2.656)
  Mean delta:    0.013 (Z=  0.652)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.60    -6.20  1.40e+00  1.96e+01   4.4*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.47     5.73  1.30e+00  1.94e+01   4.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   116.71    -4.11  1.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.966 (Z=  4.430)
  Mean delta:    1.755 (Z=  0.985)

                      ----------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   157.95    22.05  5.00e+00  1.95e+01   4.4*sigma

  Min. delta:    0.054
  Max. delta:   89.702
  Mean delta:   12.551

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.259
  Mean delta:    0.085

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.062
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.464
    Angle     :  1.636   8.962   4079  Z= 0.731
    Chirality :  0.085   0.259    176
    Planarity :  0.009   0.048    327
    Dihedral  : 11.079  89.702    769
    Min Nonbonded Distance : 1.723
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  2.42 %
      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: -0.55 (0.65), residues: 137
    helix: -0.71 (0.45), residues: 83
    sheet: -1.09 (1.76), residues: 10
    loop :  1.05 (1.00), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A 136 
   PHE   0.050   0.009   PHE A  67 
   TYR   0.083   0.016   TYR A 111 
   ARG   0.055   0.012   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A 136 
   PHE   0.034   0.010   PHE A  67 
   TYR   0.071   0.017   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 disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.91 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   1.35
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.64
  MolProbity score      =   0.86

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: 60
        1.23 -     1.42: 412
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.32e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.84e+00
  bond model="   0" pdb=" CZ  ARG A 129 " segid="A   "
       model="   0" pdb=" NH2 ARG A 129 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.70e+00
  bond model="   0" pdb=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.55e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.401 -0.027 1.10e-02 8.26e+03 6.19e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.82 -   105.96: 96
      105.96 -   112.10: 2516
      112.10 -   118.24: 511
      118.24 -   124.37: 864
      124.37 -   130.51: 92
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  117.93    4.67 1.00e+00 1.00e+00 2.18e+01
  angle model="   0" pdb=" OE1 GLN A 100 " segid="A   "
        model="   0" pdb=" CD  GLN A 100 " segid="A   "
        model="   0" pdb=" NE2 GLN A 100 " segid="A   "
      ideal   model   delta    sigma   weight residual
     122.60  118.19    4.41 1.00e+00 1.00e+00 1.94e+01
  angle model="   0" pdb=" CD  ARG A 129 " segid="A   "
        model="   0" pdb=" NE  ARG A 129 " segid="A   "
        model="   0" pdb=" CZ  ARG A 129 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  130.51   -6.11 1.40e+00 5.10e-01 1.91e+01
  angle model="   0" pdb=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  129.41   -5.01 1.40e+00 5.10e-01 1.28e+01
  angle model="   0" pdb=" OE1 GLN A  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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 -    17.99: 961
       17.99 -    35.98: 50
       35.98 -    53.97: 18
       53.97 -    71.95: 1
       71.95 -    89.94: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 " segid="A   "
           model="   0" pdb=" C   THR A  83 " segid="A   "
           model="   0" pdb=" N   GLU A  84 " segid="A   "
           model="   0" pdb=" CA  GLU A  84 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.69   21.31     0      5.00e+00 4.00e-02 1.82e+01
  dihedral model="   0" pdb=" CA  THR A  82 " segid="A   "
           model="   0" pdb=" C   THR A  82 " segid="A   "
           model="   0" pdb=" N   THR A  83 " segid="A   "
           model="   0" pdb=" CA  THR A  83 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.57   19.43     0      5.00e+00 4.00e-02 1.51e+01
  dihedral model="   0" pdb=" CA  TYR A  81 " segid="A   "
           model="   0" pdb=" C   TYR A  81 " segid="A   "
           model="   0" pdb=" N   THR A  82 " segid="A   "
           model="   0" pdb=" CA  THR A  82 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.23   15.77     0      5.00e+00 4.00e-02 9.95e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 70
       0.048 -    0.096: 58
       0.096 -    0.145: 37
       0.145 -    0.193: 10
       0.193 -    0.241: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    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=" CG  LEU A 119 " segid="A   "
            model="   0" pdb=" CB  LEU A 119 " segid="A   "
            model="   0" pdb=" CD1 LEU A 119 " segid="A   "
            model="   0" pdb=" CD2 LEU A 119 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.19 2.00e-01 2.50e+01 8.91e-01
  chirality model="   0" pdb=" CA  PRO A  54 " segid="A   "
            model="   0" pdb=" N   PRO A  54 " segid="A   "
            model="   0" pdb=" C   PRO A  54 " segid="A   "
            model="   0" pdb=" CB  PRO A  54 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.49e-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 " segid="A   "    0.069 2.00e-02 2.50e+03   3.45e-02 3.57e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "    0.025 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.074 2.00e-02 2.50e+03   3.35e-02 3.37e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.070 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 " segid="A   "   -0.037 2.00e-02 2.50e+03   3.02e-02 2.73e+01
        model="   0" pdb=" CG  TYR A  68 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 " segid="A   "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 " segid="A   "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 " segid="A   "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 " segid="A   "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 " segid="A   "   -0.078 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 " segid="A   "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 " segid="A   "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 " segid="A   "    0.044 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 394
        2.32 -     2.89: 5225
        2.89 -     3.46: 5489
        3.46 -     4.03: 7313
        4.03 -     4.60: 10628
  Nonbonded interactions: 29049
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.746 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 " segid="A   "
            model="   0" pdb=" OD1 ASP A  23 " segid="A   "
     model   vdw
     1.776 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 " segid="A   "
            model="   0" pdb=" HG  SER A  46 " segid="A   "
     model   vdw
     1.780 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.783 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.794 1.730
  ... (remaining 29044 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.788)
  Mean delta:    0.012 (Z=  0.617)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.06     4.54  1.00e+00  2.06e+01   4.5*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.90     5.30  1.30e+00  1.66e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.878 (Z=  4.539)
  Mean delta:    1.690 (Z=  0.954)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   158.33    21.67  5.00e+00  1.88e+01   4.3*sigma

  Min. delta:    0.033
  Max. delta:   87.224
  Mean delta:   11.929

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.234
  Mean delta:    0.078

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.158
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.439
    Angle     :  1.586   8.878   4079  Z= 0.709
    Chirality :  0.078   0.234    176
    Planarity :  0.012   0.121    327
    Dihedral  : 11.050  87.224    769
    Min Nonbonded Distance : 1.701
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.28 (0.66), residues: 137
    helix: -1.09 (0.51), residues: 76
    sheet: -1.35 (1.62), residues: 10
    loop :  0.02 (0.89), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A 135 
   PHE   0.055   0.011   PHE A  67 
   TYR   0.104   0.016   TYR A  91 
   ARG   0.123   0.025   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A 135 
   PHE   0.038   0.011   PHE A  67 
   TYR   0.057   0.014   TYR A  81 
   ARG   0.018   0.003   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:    0.041 (Z=  3.158)
  Mean delta:    0.013 (Z=  0.673)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.08     5.52  1.00e+00  3.05e+01   5.5*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   131.24    -6.84  1.40e+00  2.39e+01   4.9*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.20     4.40  1.00e+00  1.94e+01   4.4*sigma

  Min. delta:    0.006 (Z=  0.005)
  Max. delta:    7.592 (Z=  5.519)
  Mean delta:    1.796 (Z=  1.002)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.063
  Max. delta:   78.421
  Mean delta:   12.174

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.234
  Mean delta:    0.084

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.140
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2242  Z= 0.479
    Angle     :  1.662   7.592   4079  Z= 0.742
    Chirality :  0.084   0.234    176
    Planarity :  0.011   0.105    327
    Dihedral  : 11.878  80.070    769
    Min Nonbonded Distance : 1.401
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.14 (0.67), residues: 137
    helix: -1.18 (0.45), residues: 90
    sheet: -1.58 (1.38), residues: 10
    loop :  1.36 (1.18), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.040   0.008   PHE A  67 
   TYR   0.071   0.015   TYR A  12 
   ARG   0.113   0.023   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.027   0.007   PHE A  67 
   TYR   0.060   0.015   TYR A  12 
   ARG   0.013   0.003   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.59
  MolProbity score      =   0.90

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   1.35
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.66
  MolProbity score      =   1.11

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=  2.638)
  Mean delta:    0.013 (Z=  0.657)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.79     4.81  1.00e+00  2.31e+01   4.8*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.088 (Z=  4.809)
  Mean delta:    1.802 (Z=  0.994)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   75.142
  Mean delta:   13.035

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.237
  Mean delta:    0.083

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.085
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.665   8.088   4079  Z= 0.738
    Chirality :  0.083   0.237    176
    Planarity :  0.010   0.064    327
    Dihedral  : 11.767  80.072    769
    Min Nonbonded Distance : 1.708
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.40 (0.65), residues: 137
    helix: -1.16 (0.44), residues: 86
    sheet: -2.73 (1.07), residues: 10
    loop :  0.71 (1.13), residues: 41
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.026   0.006   PHE A  67 
   TYR   0.081   0.015   TYR A  12 
   ARG   0.070   0.016   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.019   0.005   PHE A  67 
   TYR   0.068   0.017   TYR A  12 
   ARG   0.006   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.735)
  Mean delta:    0.013 (Z=  0.662)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.91     4.69  1.00e+00  2.20e+01   4.7*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.925 (Z=  4.686)
  Mean delta:    1.798 (Z=  0.988)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   146.97    33.03  5.00e+00  4.36e+01   6.6*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   153.08    26.92  5.00e+00  2.90e+01   5.4*sigma

  Min. delta:    0.007
  Max. delta:   76.575
  Mean delta:   13.054

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.229
  Mean delta:    0.085

                       ----------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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.471
    Angle     :  1.673   7.925   4079  Z= 0.738
    Chirality :  0.085   0.229    176
    Planarity :  0.010   0.058    327
    Dihedral  : 12.026  78.063    769
    Min Nonbonded Distance : 1.735
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  3.65 %
      Favored  : 94.89 %
    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 : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.01 (0.71), residues: 137
    helix: -1.02 (0.48), residues: 89
    sheet: -2.27 (1.44), residues: 10
    loop :  1.43 (1.22), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.052   0.010   PHE A  67 
   TYR   0.082   0.015   TYR A  12 
   ARG   0.063   0.014   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.035   0.009   PHE A  67 
   TYR   0.070   0.017   TYR A  12 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.661)
  Mean delta:    0.013 (Z=  0.656)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.94     4.66  1.00e+00  2.17e+01   4.7*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.307 (Z=  4.661)
  Mean delta:    1.811 (Z=  0.995)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   145.49    34.51  5.00e+00  4.76e+01   6.9*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   156.37    23.63  5.00e+00  2.23e+01   4.7*sigma

  Min. delta:    0.004
  Max. delta:   78.208
  Mean delta:   13.368

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.236
  Mean delta:    0.086

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.079
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.467
    Angle     :  1.681   7.307   4079  Z= 0.742
    Chirality :  0.086   0.236    176
    Planarity :  0.010   0.061    327
    Dihedral  : 11.339  78.208    769
    Min Nonbonded Distance : 1.727
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.11 %
      Favored  : 92.70 %
    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: -1.68 (0.69), residues: 137
    helix: -1.53 (0.47), residues: 78
    sheet: -1.30 (1.65), residues: 10
    loop :  0.11 (1.07), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.005   HIS A  43 
   PHE   0.049   0.010   PHE A  67 
   TYR   0.095   0.017   TYR A  68 
   ARG   0.069   0.016   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.005   HIS A  43 
   PHE   0.034   0.009   PHE A  67 
   TYR   0.073   0.018   TYR A  68 
   ARG   0.006   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  94.89 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.67
  MolProbity score      =   1.01

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.19 %
                favored =  92.70 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   1.35
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.68
  MolProbity score      =   1.48

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


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=  2.645)
  Mean delta:    0.013 (Z=  0.652)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma
   A  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:    0.001 (Z=  0.001)
  Max. delta:    8.034 (Z=  4.160)
  Mean delta:    1.757 (Z=  0.969)

                      ----------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   158.30    21.70  5.00e+00  1.88e+01   4.3*sigma

  Min. delta:    0.005
  Max. delta:   77.056
  Mean delta:   13.192

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.234
  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:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.464
    Angle     :  1.632   8.034   4079  Z= 0.722
    Chirality :  0.079   0.234    176
    Planarity :  0.010   0.057    327
    Dihedral  : 12.015  89.955    769
    Min Nonbonded Distance : 1.748
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  0.81 %
      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: -1.31 (0.67), residues: 137
    helix: -1.03 (0.45), residues: 92
    sheet: -2.74 (1.08), residues: 10
    loop :  0.97 (1.26), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.021   0.006   PHE A  67 
   TYR   0.069   0.016   TYR A 111 
   ARG   0.063   0.020   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.062   0.017   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 =  96.35 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.66
  MolProbity score      =   1.31

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0090
  RMS(angles)           =   1.63
  MolProbity score      =   1.29

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=  2.975)
  Mean delta:    0.013 (Z=  0.641)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:    8.359 (Z=  3.820)
  Mean delta:    1.656 (Z=  0.929)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.037
  Max. delta:   73.101
  Mean delta:   10.540

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  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:    0.092
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.457
    Angle     :  1.563   8.359   4079  Z= 0.694
    Chirality :  0.074   0.200    176
    Planarity :  0.010   0.067    327
    Dihedral  : 10.637  73.101    769
    Min Nonbonded Distance : 1.691
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    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: -1.32 (0.62), residues: 137
    helix: -1.17 (0.44), residues: 85
    sheet: -0.73 (1.54), residues: 10
    loop :  0.28 (0.96), residues: 42
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.005   HIS A 135 
   PHE   0.046   0.008   PHE A  67 
   TYR   0.063   0.014   TYR A  91 
   ARG   0.072   0.023   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.005   HIS A 135 
   PHE   0.032   0.009   PHE A  67 
   TYR   0.052   0.013   TYR A 111 
   ARG   0.017   0.003   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A 135  HIS
   A 138  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=  2.767)
  Mean delta:    0.013 (Z=  0.659)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.25     4.35  1.00e+00  1.89e+01   4.3*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.27     4.33  1.00e+00  1.87e+01   4.3*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.34     4.26  1.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:    7.900 (Z=  4.346)
  Mean delta:    1.776 (Z=  0.979)

                      ----------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  -156.00   -24.00  5.00e+00  2.30e+01   4.8*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   156.10    23.90  5.00e+00  2.29e+01   4.8*sigma

  Min. delta:    0.067
  Max. delta:   77.251
  Mean delta:   12.861

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.220
  Mean delta:    0.084

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.103
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.659   7.900   4079  Z= 0.732
    Chirality :  0.084   0.220    176
    Planarity :  0.011   0.079    327
    Dihedral  : 11.244  77.251    769
    Min Nonbonded Distance : 1.724
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.44 (0.66), residues: 137
    helix: -1.15 (0.45), residues: 89
    sheet: -1.27 (1.46), residues: 10
    loop :  0.29 (1.16), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.004   HIS A  43 
   PHE   0.045   0.009   PHE A  67 
   TYR   0.068   0.016   TYR A  68 
   ARG   0.086   0.025   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.018   0.004   HIS A  43 
   PHE   0.031   0.007   PHE A  67 
   TYR   0.059   0.016   TYR A 111 
   ARG   0.013   0.003   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            =   0.00
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.56
  MolProbity score      =   0.54

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.66
  MolProbity score      =   0.90

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.656)
  Mean delta:    0.012 (Z=  0.628)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   108.06     4.54  1.00e+00  2.06e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.29     4.31  1.00e+00  1.86e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.311 (Z=  4.543)
  Mean delta:    1.626 (Z=  0.920)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   88.433
  Mean delta:   15.820

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.194
  Mean delta:    0.070

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.057
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2242  Z= 0.447
    Angle     :  1.545   7.311   4079  Z= 0.688
    Chirality :  0.070   0.194    176
    Planarity :  0.009   0.044    327
    Dihedral  : 13.563  88.433    769
    Min Nonbonded Distance : 1.793
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.73 %
      Favored  : 99.27 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.81 %
      Favored  : 98.39 %
    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: -1.91 (0.66), residues: 137
    helix: -1.42 (0.48), residues: 82
    sheet: -3.17 (1.13), residues: 10
    loop :  0.04 (1.00), residues: 45
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.005   HIS A 139 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.098   0.016   TYR A 111 
   ARG   0.049   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.005   HIS A 139 
   PHE   0.009   0.003   PHE A  67 
   TYR   0.082   0.015   TYR A 111 
   ARG   0.004   0.002   ARG A 129 

                     ----------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:    0.038 (Z=  2.659)
  Mean delta:    0.013 (Z=  0.657)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.53     4.07  1.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    8.563 (Z=  4.172)
  Mean delta:    1.769 (Z=  0.981)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   76.828
  Mean delta:   13.270

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.253
  Mean delta:    0.082

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.100       0.173      199.92   8.7*sigma
   A 111  TYR  CB
   A 111  TYR  CG
   A 111  TYR  CD1
   A 111  TYR  CD2
   A 111  TYR  CE1
   A 111  TYR  CE2
   A 111  TYR  CZ
   A 111  TYR  OH            0.043       0.083       36.76   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.100
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.649   8.563   4079  Z= 0.731
    Chirality :  0.082   0.253    176
    Planarity :  0.011   0.094    327
    Dihedral  : 11.852  76.828    769
    Min Nonbonded Distance : 1.708
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  5.65 %
      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: -0.67 (0.70), residues: 137
    helix: -0.82 (0.45), residues: 91
    sheet: -0.76 (1.61), residues: 10
    loop :  1.40 (1.31), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A 139 
   PHE   0.048   0.009   PHE A  67 
   TYR   0.208   0.024   TYR A  50 
   ARG   0.076   0.016   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.009   0.003   HIS A 139 
   PHE   0.033   0.008   PHE A  67 
   TYR   0.173   0.028   TYR A  50 
   ARG   0.005   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:    0.038 (Z=  2.790)
  Mean delta:    0.013 (Z=  0.675)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.01     4.59  1.00e+00  2.11e+01   4.6*sigma

  Min. delta:    0.004 (Z=  0.003)
  Max. delta:    7.949 (Z=  4.593)
  Mean delta:    1.779 (Z=  0.990)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.032
  Max. delta:   76.751
  Mean delta:   11.769

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.205
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.091
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.480
    Angle     :  1.653   7.949   4079  Z= 0.735
    Chirality :  0.082   0.205    176
    Planarity :  0.010   0.070    327
    Dihedral  : 10.364  76.751    769
    Min Nonbonded Distance : 1.724
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.73 %
      Favored  : 99.27 %
    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: -1.72 (0.66), residues: 137
    helix: -1.74 (0.45), residues: 88
    sheet: -0.25 (1.59), residues: 10
    loop :  0.79 (1.07), residues: 39
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.061   0.010   PHE A  67 
   TYR   0.074   0.015   TYR A  68 
   ARG   0.076   0.016   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.004   HIS A  43 
   PHE   0.042   0.010   PHE A  67 
   TYR   0.057   0.015   TYR A  68 
   ARG   0.003   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 134  HIS

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  99.27 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   1.80
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.55
  MolProbity score      =   0.94

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.652)
  Mean delta:    0.013 (Z=  0.661)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.81     4.79  1.00e+00  2.30e+01   4.8*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.47    -6.07  1.40e+00  1.88e+01   4.3*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.95     5.25  1.30e+00  1.63e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    8.400 (Z=  4.792)
  Mean delta:    1.812 (Z=  1.009)

                      ----------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   149.61    30.39  5.00e+00  3.69e+01   6.1*sigma

  Min. delta:    0.074
  Max. delta:   77.174
  Mean delta:   13.140

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.232
  Mean delta:    0.084

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.093       0.170      174.46   8.5*sigma

  Min. delta:    0.000
  Max. delta:    0.096
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.471
    Angle     :  1.670   8.400   4079  Z= 0.746
    Chirality :  0.084   0.232    176
    Planarity :  0.012   0.087    327
    Dihedral  : 12.001  77.174    769
    Min Nonbonded Distance : 1.733
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    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 : 0.76 %
  
  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: -0.82 (0.70), residues: 137
    helix: -0.93 (0.46), residues: 89
    sheet: -1.07 (1.78), residues: 10
    loop :  1.28 (1.22), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.041   0.008   PHE A  67 
   TYR   0.202   0.022   TYR A  50 
   ARG   0.079   0.020   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.003   HIS A  43 
   PHE   0.028   0.007   PHE A  67 
   TYR   0.170   0.023   TYR A  50 
   ARG   0.008   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.65
  MolProbity score      =   1.06

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  99.27 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0094
  RMS(angles)           =   1.65
  MolProbity score      =   0.66

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.67
  MolProbity score      =   0.95

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: ""

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=  2.744)
  Mean delta:    0.013 (Z=  0.659)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.09     4.51  1.00e+00  2.04e+01   4.5*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.698 (Z=  4.511)
  Mean delta:    1.794 (Z=  0.981)

                      ----------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  -152.89   -27.11  5.00e+00  2.94e+01   5.4*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   154.11    25.89  5.00e+00  2.68e+01   5.2*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   154.77    25.23  5.00e+00  2.55e+01   5.0*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   156.48    23.52  5.00e+00  2.21e+01   4.7*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   159.31    20.69  5.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.009
  Max. delta:   77.919
  Mean delta:   12.887

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.233
  Mean delta:    0.084

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  50  TYR  CB
   A  50  TYR  CG
   A  50  TYR  CD1
   A  50  TYR  CD2
   A  50  TYR  CE1
   A  50  TYR  CE2
   A  50  TYR  CZ
   A  50  TYR  OH            0.045       0.089       40.64   4.5*sigma
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.086       0.086      146.44   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.101
  Mean delta:    0.017

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.666   7.698   4079  Z= 0.733
    Chirality :  0.084   0.233    176
    Planarity :  0.012   0.088    327
    Dihedral  : 11.374  77.919    769
    Min Nonbonded Distance : 1.719
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  4.38 %
      Favored  : 92.70 %
    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: -1.74 (0.69), residues: 137
    helix: -1.14 (0.46), residues: 90
    sheet: -1.39 (1.45), residues: 10
    loop : -0.53 (1.28), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.004   HIS A  43 
   PHE   0.025   0.007   PHE A  67 
   TYR   0.196   0.026   TYR A  91 
   ARG   0.083   0.023   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.023   0.004   HIS A  43 
   PHE   0.016   0.005   PHE A  67 
   TYR   0.153   0.028   TYR A  91 
   ARG   0.008   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.92 %
                favored =  92.70 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.67
  MolProbity score      =   1.12

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.037 (Z=  2.698)
  Mean delta:    0.012 (Z=  0.623)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.612 (Z=  4.112)
  Mean delta:    1.732 (Z=  0.965)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.025
  Max. delta:   86.421
  Mean delta:   15.764

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.282
  Mean delta:    0.089

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.128
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.444
    Angle     :  1.626   8.147   4079  Z= 0.721
    Chirality :  0.089   0.282    176
    Planarity :  0.010   0.093    327
    Dihedral  : 13.612  86.421    769
    Min Nonbonded Distance : 1.775
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  5.11 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  2.42 %
      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: -2.33 (0.67), residues: 137
    helix: -1.44 (0.51), residues: 70
    sheet: -2.57 (1.35), residues: 10
    loop : -1.25 (0.90), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.004   HIS A  43 
   PHE   0.026   0.007   PHE A  67 
   TYR   0.053   0.015   TYR A 111 
   ARG   0.100   0.018   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.016   0.004   HIS A  43 
   PHE   0.016   0.005   PHE A  67 
   TYR   0.044   0.015   TYR A  91 
   ARG   0.020   0.003   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  93.43 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   1.35
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.63
  MolProbity score      =   1.29

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}
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.818, 64.271, 61.437, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       2     16.00
     O1-    25      9.00
     O     192      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:    0.038 (Z=  2.665)
  Mean delta:    0.013 (Z=  0.669)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.23     4.37  1.00e+00  1.91e+01   4.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.30     4.30  1.00e+00  1.85e+01   4.3*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.218 (Z=  4.366)
  Mean delta:    1.797 (Z=  0.993)

                      ----------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  -159.94   -20.06  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.032
  Max. delta:   85.466
  Mean delta:   13.596

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.236
  Mean delta:    0.083

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.080
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.477
    Angle     :  1.673   8.218   4079  Z= 0.740
    Chirality :  0.083   0.236    176
    Planarity :  0.010   0.062    327
    Dihedral  : 12.406  85.466    769
    Min Nonbonded Distance : 1.713
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  5.65 %
      Favored  : 91.94 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.61 (0.67), residues: 137
    helix: -1.37 (0.46), residues: 86
    sheet: -1.47 (1.55), residues: 10
    loop :  0.32 (1.10), residues: 41
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.044   0.009   PHE A  67 
   TYR   0.110   0.019   TYR A  91 
   ARG   0.069   0.015   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.030   0.009   PHE A  67 
   TYR   0.089   0.022   TYR A  91 
   ARG   0.004   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  3.094)
  Mean delta:    0.012 (Z=  0.624)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   107.83     4.77  1.00e+00  2.28e+01   4.8*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   107.85     4.75  1.00e+00  2.26e+01   4.8*sigma
   A 136  HIS  CB
   A 136  HIS  CG
   A 136  HIS  CD2       131.20   125.20     6.00  1.30e+00  2.13e+01   4.6*sigma
   A  58  ARG  CD
   A  58  ARG  NE
   A  58  ARG  CZ        124.40   130.06    -5.66  1.40e+00  1.63e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    6.778 (Z=  4.775)
  Mean delta:    1.720 (Z=  0.978)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   155.73    24.27  5.00e+00  2.36e+01   4.9*sigma

  Min. delta:    0.008
  Max. delta:   88.634
  Mean delta:   16.636

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.282
  Mean delta:    0.079

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.063
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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     :  1.621   7.310   4079  Z= 0.727
    Chirality :  0.079   0.282    176
    Planarity :  0.009   0.049    327
    Dihedral  : 14.247  88.634    769
    Min Nonbonded Distance : 1.730
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  5.65 %
      Favored  : 93.55 %
    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: -1.89 (0.71), residues: 137
    helix: -1.80 (0.49), residues: 69
    sheet: -3.38 (1.04), residues: 10
    loop :  0.23 (0.98), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.007   HIS A 137 
   PHE   0.050   0.011   PHE A  67 
   TYR   0.091   0.013   TYR A 111 
   ARG   0.054   0.006   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.007   HIS A 137 
   PHE   0.034   0.012   PHE A  67 
   TYR   0.077   0.012   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 =  96.35 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.67
  MolProbity score      =   1.31

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.62
  MolProbity score      =   1.01

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.038 (Z=  2.719)
  Mean delta:    0.013 (Z=  0.668)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.13     4.47  1.00e+00  2.00e+01   4.5*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.39     4.21  1.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.046 (Z=  4.471)
  Mean delta:    1.793 (Z=  0.984)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   153.13    26.87  5.00e+00  2.89e+01   5.4*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   155.55    24.45  5.00e+00  2.39e+01   4.9*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   159.08    20.92  5.00e+00  1.75e+01   4.2*sigma

  Min. delta:    0.013
  Max. delta:   78.482
  Mean delta:   12.303

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.259
  Mean delta:    0.089

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.076
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.476
    Angle     :  1.671   8.046   4079  Z= 0.736
    Chirality :  0.089   0.259    176
    Planarity :  0.010   0.059    327
    Dihedral  : 11.165  78.482    769
    Min Nonbonded Distance : 1.693
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    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: -1.64 (0.66), residues: 137
    helix: -1.48 (0.46), residues: 83
    sheet: -0.98 (1.63), residues: 10
    loop :  0.23 (1.04), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.043   0.009   PHE A  67 
   TYR   0.085   0.017   TYR A  50 
   ARG   0.067   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.029   0.007   PHE A  67 
   TYR   0.070   0.016   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:    0.038 (Z=  2.627)
  Mean delta:    0.013 (Z=  0.661)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        121.70   133.18   -11.48  1.80e+00  4.07e+01   6.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.96     4.64  1.00e+00  2.16e+01   4.6*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.16     4.44  1.00e+00  1.97e+01   4.4*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   116.88    -4.28  1.00e+00  1.83e+01   4.3*sigma
   A 116  ASP  C
   A 116  ASP  CA
   A 116  ASP  CB        110.10   117.87    -7.77  1.90e+00  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   11.482 (Z=  6.379)
  Mean delta:    1.877 (Z=  1.027)

                      ----------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   145.71    34.29  5.00e+00  4.70e+01   6.9*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   152.27    27.73  5.00e+00  3.08e+01   5.5*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   154.94    25.06  5.00e+00  2.51e+01   5.0*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   155.11    24.89  5.00e+00  2.48e+01   5.0*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   156.86    23.14  5.00e+00  2.14e+01   4.6*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   159.19    20.81  5.00e+00  1.73e+01   4.2*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   159.64    20.36  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.037
  Max. delta:   78.835
  Mean delta:   12.052

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.247
  Mean delta:    0.085

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.080
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.471
    Angle     :  1.725  11.482   4079  Z= 0.762
    Chirality :  0.085   0.247    176
    Planarity :  0.010   0.060    327
    Dihedral  : 11.135  80.018    769
    Min Nonbonded Distance : 1.705
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  8.03 %
      Favored  : 89.05 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.81 %
      Favored  : 97.58 %
    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: -2.40 (0.67), residues: 137
    helix: -1.92 (0.46), residues: 76
    sheet: -1.33 (1.74), residues: 10
    loop : -0.74 (1.00), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.022   0.006   PHE A  67 
   TYR   0.085   0.015   TYR A  68 
   ARG   0.067   0.013   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.012   0.004   PHE A  67 
   TYR   0.066   0.016   TYR A  68 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.67
  MolProbity score      =   0.80

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:    0.037 (Z=  2.801)
  Mean delta:    0.013 (Z=  0.661)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.21     4.39  1.00e+00  1.93e+01   4.4*sigma
   A  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:    0.004 (Z=  0.003)
  Max. delta:    7.995 (Z=  4.389)
  Mean delta:    1.773 (Z=  0.974)

                      ----------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   146.40    33.60  5.00e+00  4.52e+01   6.7*sigma

  Min. delta:    0.017
  Max. delta:   77.771
  Mean delta:   12.908

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.239
  Mean delta:    0.088

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.093
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.470
    Angle     :  1.664   7.995   4079  Z= 0.731
    Chirality :  0.088   0.239    176
    Planarity :  0.010   0.071    327
    Dihedral  : 12.042  88.971    769
    Min Nonbonded Distance : 1.729
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    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 : 0.76 %
  
  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: -0.90 (0.68), residues: 137
    helix: -1.22 (0.45), residues: 86
    sheet: -1.63 (1.53), residues: 10
    loop :  1.78 (1.13), residues: 41
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.043   0.009   PHE A  67 
   TYR   0.088   0.017   TYR A  68 
   ARG   0.079   0.017   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.030   0.008   PHE A  67 
   TYR   0.067   0.018   TYR A  68 
   ARG   0.003   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.038 (Z=  2.679)
  Mean delta:    0.013 (Z=  0.660)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.90     4.70  1.00e+00  2.21e+01   4.7*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.103 (Z=  4.702)
  Mean delta:    1.739 (Z=  0.958)

                      ----------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   159.46    20.54  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.045
  Max. delta:   78.631
  Mean delta:   12.285

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:    0.232
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.076
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.470
    Angle     :  1.627   8.103   4079  Z= 0.717
    Chirality :  0.082   0.232    176
    Planarity :  0.010   0.058    327
    Dihedral  : 11.466  89.973    769
    Min Nonbonded Distance : 1.733
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -1.38 (0.65), residues: 137
    helix: -1.22 (0.43), residues: 90
    sheet: -2.12 (1.35), residues: 10
    loop :  0.97 (1.19), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.046   0.008   PHE A  67 
   TYR   0.099   0.017   TYR A  68 
   ARG   0.063   0.016   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.030   0.007   PHE A  67 
   TYR   0.078   0.018   TYR A  68 
   ARG   0.005   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.668)
  Mean delta:    0.013 (Z=  0.657)

                        ----------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  1.66e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.698 (Z=  4.077)
  Mean delta:    1.765 (Z=  0.976)

                      ----------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   148.70    31.30  5.00e+00  3.92e+01   6.3*sigma

  Min. delta:    0.050
  Max. delta:   78.339
  Mean delta:   12.975

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.263
  Mean delta:    0.083

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.099
  Mean delta:    0.016

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================

  Ramachandran outliers =   2.92 %
                favored =  89.05 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0093
  RMS(angles)           =   1.72
  MolProbity score      =   1.39

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.650   7.698   4079  Z= 0.729
    Chirality :  0.083   0.263    176
    Planarity :  0.011   0.077    327
    Dihedral  : 11.515  80.076    769
    Min Nonbonded Distance : 1.704
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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 : 0.76 %
  
  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: -0.44 (0.69), residues: 137
    helix: -0.53 (0.47), residues: 90
    sheet: -2.05 (1.53), residues: 10
    loop :  1.56 (1.19), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.044   0.008   PHE A  67 
   TYR   0.069   0.018   TYR A  68 
   ARG   0.086   0.023   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.030   0.008   PHE A  67 
   TYR   0.062   0.017   TYR A 111 
   ARG   0.007   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   0.80

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.63
  MolProbity score      =   0.74

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.65
  MolProbity score      =   1.19

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.037 (Z=  2.603)
  Mean delta:    0.013 (Z=  0.653)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.79     4.81  1.00e+00  2.31e+01   4.8*sigma
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.96     5.24  1.30e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.337 (Z=  4.811)
  Mean delta:    1.824 (Z=  1.004)

                      ----------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   144.77    35.23  5.00e+00  4.97e+01   7.0*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   154.74    25.26  5.00e+00  2.55e+01   5.1*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   158.09    21.91  5.00e+00  1.92e+01   4.4*sigma

  Min. delta:    0.008
  Max. delta:   77.553
  Mean delta:   13.126

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.227
  Mean delta:    0.084

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.074
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.465
    Angle     :  1.672   8.337   4079  Z= 0.743
    Chirality :  0.084   0.227    176
    Planarity :  0.010   0.057    327
    Dihedral  : 11.326  77.553    769
    Min Nonbonded Distance : 1.699
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  5.11 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  4.84 %
      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: -1.25 (0.73), residues: 137
    helix: -1.20 (0.50), residues: 84
    sheet: -1.85 (1.68), residues: 10
    loop :  0.81 (1.19), residues: 43
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.025   0.007   PHE A  45 
   TYR   0.059   0.013   TYR A 111 
   ARG   0.061   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.056   0.013   TYR A 111 
   ARG   0.006   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  93.43 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   1.80
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.67
  MolProbity score      =   1.37

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=  2.773)
  Mean delta:    0.013 (Z=  0.662)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.78     4.82  1.00e+00  2.32e+01   4.8*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.91    -6.51  1.40e+00  2.16e+01   4.7*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.03     4.57  1.00e+00  2.08e+01   4.6*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.670 (Z=  4.816)
  Mean delta:    1.782 (Z=  0.988)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   155.79    24.21  5.00e+00  2.35e+01   4.8*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   159.25    20.75  5.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.007
  Max. delta:   78.680
  Mean delta:   12.140

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.222
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.071
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.471
    Angle     :  1.653   7.670   4079  Z= 0.734
    Chirality :  0.082   0.222    176
    Planarity :  0.010   0.054    327
    Dihedral  : 11.230  78.680    769
    Min Nonbonded Distance : 1.737
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.81 %
      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: -1.16 (0.68), residues: 137
    helix: -1.13 (0.45), residues: 89
    sheet: -2.18 (1.45), residues: 10
    loop :  1.30 (1.22), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A  43 
   PHE   0.051   0.009   PHE A  67 
   TYR   0.076   0.016   TYR A  68 
   ARG   0.058   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.005   HIS A  43 
   PHE   0.035   0.009   PHE A  67 
   TYR   0.061   0.017   TYR A 111 
   ARG   0.007   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A 137  HIS

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   1.35
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   1.33

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: 1.07
  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.

  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=" CD2 HIS A 139 " segid="A   "
       model="   0" pdb=" NE2 HIS A 139 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.403 -0.029 1.10e-02 8.26e+03 6.85e+00
  bond model="   0" pdb=" CZ  ARG A  21 " segid="A   "
       model="   0" pdb=" NH2 ARG A  21 " segid="A   "
    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=" CD2 HIS A 137 " segid="A   "
       model="   0" pdb=" NE2 HIS A 137 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.36e+00
  bond model="   0" pdb=" CD2 HIS A 138 " segid="A   "
       model="   0" pdb=" NE2 HIS A 138 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.31e+00
  bond model="   0" pdb=" CD2 HIS A 135 " segid="A   "
       model="   0" pdb=" NE2 HIS A 135 " segid="A   "
    ideal  model  delta    sigma   weight residual
    1.374  1.400 -0.026 1.10e-02 8.26e+03 5.76e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.00 -   105.79: 86
      105.79 -   111.59: 2397
      111.59 -   117.38: 577
      117.38 -   123.17: 811
      123.17 -   128.96: 208
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 " segid="A   "
        model="   0" pdb=" CB  ASP A  36 " segid="A   "
        model="   0" pdb=" CG  ASP A  36 " segid="A   "
      ideal   model   delta    sigma   weight residual
     112.60  117.17   -4.57 1.00e+00 1.00e+00 2.09e+01
  angle model="   0" pdb=" OE1 GLN A  28 " segid="A   "
        model="   0" pdb=" CD  GLN A  28 " segid="A   "
        model="   0" pdb=" NE2 GLN A  28 " segid="A   "
      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  43 " segid="A   "
        model="   0" pdb=" CG  HIS A  43 " segid="A   "
        model="   0" pdb=" CD2 HIS A  43 " segid="A   "
      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  66 " segid="A   "
        model="   0" pdb=" CD  GLN A  66 " segid="A   "
        model="   0" pdb=" NE2 GLN A  66 " segid="A   "
      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=" CD  ARG A  21 " segid="A   "
        model="   0" pdb=" NE  ARG A  21 " segid="A   "
        model="   0" pdb=" CZ  ARG A  21 " segid="A   "
      ideal   model   delta    sigma   weight residual
     124.40  128.96   -4.56 1.40e+00 5.10e-01 1.06e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 966
       17.99 -    35.97: 44
       35.97 -    53.96: 16
       53.96 -    71.94: 4
       71.94 -    89.93: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LEU A 119 " segid="A   "
           model="   0" pdb=" C   LEU A 119 " segid="A   "
           model="   0" pdb=" N   GLU A 120 " segid="A   "
           model="   0" pdb=" CA  GLU A 120 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.95   25.05     0      5.00e+00 4.00e-02 2.51e+01
  dihedral model="   0" pdb=" CA  HIS A 137 " segid="A   "
           model="   0" pdb=" C   HIS A 137 " segid="A   "
           model="   0" pdb=" N   HIS A 138 " segid="A   "
           model="   0" pdb=" CA  HIS A 138 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.83   22.17     0      5.00e+00 4.00e-02 1.97e+01
  dihedral model="   0" pdb=" CA  ASP A 118 " segid="A   "
           model="   0" pdb=" C   ASP A 118 " segid="A   "
           model="   0" pdb=" N   LEU A 119 " segid="A   "
           model="   0" pdb=" CA  LEU A 119 " segid="A   "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.36   20.64     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.065: 91
       0.065 -    0.127: 61
       0.127 -    0.190: 22
       0.190 -    0.252: 0
       0.252 -    0.315: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 137 " segid="A   "
            model="   0" pdb=" N   HIS A 137 " segid="A   "
            model="   0" pdb=" C   HIS A 137 " segid="A   "
            model="   0" pdb=" CB  HIS A 137 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.47e+00
  chirality model="   0" pdb=" CA  PHE A  45 " segid="A   "
            model="   0" pdb=" N   PHE A  45 " segid="A   "
            model="   0" pdb=" C   PHE A  45 " segid="A   "
            model="   0" pdb=" CB  PHE A  45 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality model="   0" pdb=" CG  LEU A  64 " segid="A   "
            model="   0" pdb=" CB  LEU A  64 " segid="A   "
            model="   0" pdb=" CD1 LEU A  64 " segid="A   "
            model="   0" pdb=" CD2 LEU A  64 " segid="A   "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.22e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 " segid="A   "    0.066 2.00e-02 2.50e+03   2.99e-02 2.68e+01
        model="   0" pdb=" CG  TYR A  12 " segid="A   "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 " segid="A   "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 " segid="A   "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 " segid="A   "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 " segid="A   "    0.062 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 " segid="A   "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 " segid="A   "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 " segid="A   "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 " segid="A   "   -0.028 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 " segid="A   "   -0.053 2.00e-02 2.50e+03   2.98e-02 2.66e+01
        model="   0" pdb=" CG  TYR A 111 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 " segid="A   "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 " segid="A   "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 " segid="A   "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 " segid="A   "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 " segid="A   "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 " segid="A   "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 " segid="A   "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 " segid="A   "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 " segid="A   "   -0.030 2.00e-02 2.50e+03
                                                           delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 " segid="A   "   -0.020 2.00e-02 2.50e+03   2.80e-02 2.36e+01
        model="   0" pdb=" CG  TYR A  91 " segid="A   "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 " segid="A   "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 " segid="A   "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 " segid="A   "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 " segid="A   "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 " segid="A   "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 " segid="A   "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 " segid="A   "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 " segid="A   "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 " segid="A   "   -0.064 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 " segid="A   "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.30: 320
        2.30 -     2.87: 5153
        2.87 -     3.45: 5488
        3.45 -     4.02: 7294
        4.02 -     4.60: 10586
  Nonbonded interactions: 28841
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 " segid="A   "
            model="   0" pdb=" HG  SER A  76 " segid="A   "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  79 " segid="A   "
     model   vdw
     1.737 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  16 " segid="A   "
            model="   0" pdb=" HZ2 LYS A  19 " segid="A   "
     model   vdw
     1.794 1.730
  nonbonded model="   0" pdb=" OD1 ASP A  95 " segid="A   "
            model="   0" pdb=" HG  SER A  97 " segid="A   "
     model   vdw
     1.801 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 " segid="A   "
            model="   0" pdb=" HZ1 LYS A  27 " segid="A   "
     model   vdw
     1.810 1.730
  ... (remaining 28836 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=  2.725)
  Mean delta:    0.013 (Z=  0.658)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        121.70   130.36    -8.66  1.80e+00  2.32e+01   4.8*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.91     4.69  1.00e+00  2.20e+01   4.7*sigma
   A 134  HIS  CB
   A 134  HIS  CG
   A 134  HIS  CD2       131.20   125.27     5.93  1.30e+00  2.08e+01   4.6*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.32     4.28  1.00e+00  1.83e+01   4.3*sigma
   A  66  GLN  OE1
   A  66  GLN  CD
   A  66  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   116.61    -4.01  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    9.423 (Z=  4.813)
  Mean delta:    1.836 (Z=  1.015)

                      ----------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  -159.85   -20.15  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.052
  Max. delta:   77.330
  Mean delta:   13.877

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.292
  Mean delta:    0.086

                       ----------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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.704   9.423   4079  Z= 0.755
    Chirality :  0.086   0.292    176
    Planarity :  0.010   0.058    327
    Dihedral  : 12.422  80.042    769
    Min Nonbonded Distance : 1.712
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.11 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  1.61 %
      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: -1.19 (0.72), residues: 137
    helix: -1.13 (0.51), residues: 75
    sheet: -0.46 (1.77), residues: 10
    loop :  0.04 (1.03), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.036   0.008   PHE A  67 
   TYR   0.082   0.017   TYR A  12 
   ARG   0.065   0.015   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.003   HIS A  43 
   PHE   0.025   0.007   PHE A  67 
   TYR   0.069   0.016   TYR A  12 
   ARG   0.007   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  92.70 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.70
  MolProbity score      =   1.41

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=  0.002)
  Max. delta:    0.038 (Z=  2.625)
  Mean delta:    0.013 (Z=  0.667)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.93     4.67  1.00e+00  2.18e+01   4.7*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.04    -5.64  1.40e+00  1.62e+01   4.0*sigma

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:    7.739 (Z=  4.674)
  Mean delta:    1.769 (Z=  0.985)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -155.46   -24.54  5.00e+00  2.41e+01   4.9*sigma

  Min. delta:    0.002
  Max. delta:   76.510
  Mean delta:   12.247

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.232
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.079
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.475
    Angle     :  1.649   7.739   4079  Z= 0.733
    Chirality :  0.081   0.232    176
    Planarity :  0.010   0.059    327
    Dihedral  : 11.109  80.042    769
    Min Nonbonded Distance : 1.705
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.92 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.81 %
      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: -1.05 (0.67), residues: 137
    helix: -0.69 (0.47), residues: 92
    sheet: -1.64 (1.44), residues: 10
    loop :  0.22 (1.18), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.003   HIS A  43 
   PHE   0.028   0.007   PHE A  67 
   TYR   0.074   0.014   TYR A  68 
   ARG   0.065   0.017   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.014   0.003   HIS A  43 
   PHE   0.019   0.005   PHE A  67 
   TYR   0.058   0.014   TYR A  68 
   ARG   0.006   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  96.35 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.65
  MolProbity score      =   1.06

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=  2.738)
  Mean delta:    0.013 (Z=  0.659)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   130.45    -8.75  1.80e+00  2.37e+01   4.9*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.92     4.68  1.00e+00  2.19e+01   4.7*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.754 (Z=  4.863)
  Mean delta:    1.802 (Z=  0.997)

                      ----------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   153.63    26.37  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   158.54    21.46  5.00e+00  1.84e+01   4.3*sigma

  Min. delta:    0.019
  Max. delta:   78.968
  Mean delta:   13.049

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.248
  Mean delta:    0.083

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.088
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.469
    Angle     :  1.668   8.754   4079  Z= 0.740
    Chirality :  0.083   0.248    176
    Planarity :  0.010   0.068    327
    Dihedral  : 11.796  80.030    769
    Min Nonbonded Distance : 1.702
  
  Molprobity Statistics.
    All-atom Clashscore : 0.45
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    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: -0.87 (0.70), residues: 137
    helix: -0.92 (0.47), residues: 87
    sheet: -2.46 (1.45), residues: 10
    loop :  1.42 (1.18), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.039   0.009   PHE A  67 
   TYR   0.074   0.017   TYR A 111 
   ARG   0.077   0.014   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.012   0.003   HIS A  43 
   PHE   0.026   0.008   PHE A  67 
   TYR   0.065   0.018   TYR A 111 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.45
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.67
  MolProbity score      =   1.01

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:    0.037 (Z=  2.592)
  Mean delta:    0.012 (Z=  0.617)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.286 (Z=  3.893)
  Mean delta:    1.666 (Z=  0.925)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.014
  Max. delta:   81.691
  Mean delta:   11.851

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.220
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.096
  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 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.440
    Angle     :  1.582   8.286   4079  Z= 0.696
    Chirality :  0.082   0.220    176
    Planarity :  0.009   0.071    327
    Dihedral  : 11.141  81.691    769
    Min Nonbonded Distance : 1.808
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    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     : 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: -1.92 (0.64), residues: 137
    helix: -1.18 (0.53), residues: 70
    sheet: -2.58 (1.16), residues: 10
    loop : -0.88 (0.81), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.036   0.008   PHE A  67 
   TYR   0.050   0.013   TYR A 111 
   ARG   0.077   0.013   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.004   HIS A  43 
   PHE   0.026   0.007   PHE A  67 
   TYR   0.042   0.012   TYR A  12 
   ARG   0.010   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.58
  MolProbity score      =   0.50

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=  2.591)
  Mean delta:    0.013 (Z=  0.655)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.24     4.36  1.00e+00  1.90e+01   4.4*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=  0.001)
  Max. delta:    8.039 (Z=  4.363)
  Mean delta:    1.792 (Z=  0.987)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.017
  Max. delta:   77.842
  Mean delta:   12.413

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.317
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.084
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    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= 0.467
    Angle     :  1.663   8.039   4079  Z= 0.735
    Chirality :  0.082   0.317    176
    Planarity :  0.010   0.063    327
    Dihedral  : 11.385  80.034    769
    Min Nonbonded Distance : 1.703
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    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: -0.56 (0.69), residues: 137
    helix: -0.60 (0.50), residues: 84
    sheet: -2.06 (1.38), residues: 10
    loop :  1.10 (1.06), residues: 43
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.006   HIS A 137 
   PHE   0.062   0.011   PHE A  67 
   TYR   0.075   0.017   TYR A  12 
   ARG   0.069   0.019   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.022   0.006   HIS A 137 
   PHE   0.043   0.011   PHE A  67 
   TYR   0.063   0.018   TYR A  12 
   ARG   0.006   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  94.89 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   1.13

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=  0.003)
  Max. delta:    0.038 (Z=  2.706)
  Mean delta:    0.013 (Z=  0.655)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   117.93     4.67  1.00e+00  2.18e+01   4.7*sigma
   A 100  GLN  OE1
   A 100  GLN  CD
   A 100  GLN  NE2       122.60   118.19     4.41  1.00e+00  1.94e+01   4.4*sigma
   A 129  ARG  CD
   A 129  ARG  NE
   A 129  ARG  CZ        124.40   130.51    -6.11  1.40e+00  1.91e+01   4.4*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.041 (Z=  4.669)
  Mean delta:    1.795 (Z=  0.996)

                      ----------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   158.69    21.31  5.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.034
  Max. delta:   76.861
  Mean delta:   13.521

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.241
  Mean delta:    0.084

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.107
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.467
    Angle     :  1.660   7.041   4079  Z= 0.738
    Chirality :  0.084   0.241    176
    Planarity :  0.010   0.082    327
    Dihedral  : 12.226  89.942    769
    Min Nonbonded Distance : 1.746
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    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: -1.54 (0.68), residues: 137
    helix: -1.20 (0.46), residues: 92
    sheet: -2.55 (1.08), residues: 10
    loop :  0.75 (1.27), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.005   HIS A  43 
   PHE   0.058   0.010   PHE A  67 
   TYR   0.078   0.018   TYR A  68 
   ARG   0.089   0.015   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.013   0.005   HIS A  43 
   PHE   0.039   0.010   PHE A  67 
   TYR   0.063   0.018   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 =   0.00 %
                favored =  94.89 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0091
  RMS(angles)           =   1.66
  MolProbity score      =   1.28

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.037 (Z=  2.617)
  Mean delta:    0.013 (Z=  0.661)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   117.17    -4.57  1.00e+00  2.09e+01   4.6*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.912 (Z=  4.573)
  Mean delta:    1.793 (Z=  0.990)

                      ----------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   154.95    25.05  5.00e+00  2.51e+01   5.0*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   157.83    22.17  5.00e+00  1.97e+01   4.4*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   159.36    20.64  5.00e+00  1.70e+01   4.1*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   159.81    20.19  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.015
  Max. delta:   77.769
  Mean delta:   13.462

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:    0.315
  Mean delta:    0.085

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.082
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 134 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 135 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 136 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 137 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 138 " segid="A    conformer  : HE2, HD1 
    0" pdbres="HIS A 139 " segid="A    conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.470
    Angle     :  1.664   7.912   4079  Z= 0.737
    Chirality :  0.085   0.315    176
    Planarity :  0.010   0.063    327
    Dihedral  : 12.127  89.927    769
    Min Nonbonded Distance : 1.723
  
  Molprobity Statistics.
    All-atom Clashscore : 0.00
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.06 (0.68), residues: 137
    helix: -1.92 (0.42), residues: 91
    sheet: -0.82 (1.81), residues: 10
    loop :  0.80 (1.28), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A  43 
   PHE   0.058   0.011   PHE A  67 
   TYR   0.067   0.015   TYR A  50 
   ARG   0.070   0.016   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.011   0.004   HIS A  43 
   PHE   0.039   0.010   PHE A  67 
   TYR   0.056   0.015   TYR A  12 
   ARG   0.005   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  94.89 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   0.00
  RMS(bonds)            =   0.0092
  RMS(angles)           =   1.66
  MolProbity score      =   1.24

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
