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


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


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


============================== 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 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

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


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


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


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


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


  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

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

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

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

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.95, per 1000 atoms: 0.43
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (46.837, 66.606, 43.304, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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


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

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

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


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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'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 ==============================

  Time building chain proxies: 1.02, per 1000 atoms: 0.46
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.963, 65.749, 52.522, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      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: 0.76, per 1000 atoms: 0.34
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (63.089, 60.406, 42.428, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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


============================== 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

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

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

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

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

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

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

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)----------                  


  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 seconds

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


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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 88
        1.23 -     1.43: 383
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.56e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.387 -0.033 1.10e-02 8.26e+03 8.75e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.16e+00
  bond model="   0" pdb=" C   GLY A  80 "
       model="   0" pdb=" N   TYR A  81 "
    ideal  model  delta    sigma   weight residual
    1.329  1.369 -0.040 1.40e-02 5.10e+03 8.11e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.24e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.15 -   106.01: 93
      106.01 -   111.86: 2506
      111.86 -   117.71: 481
      117.71 -   123.57: 855
      123.57 -   129.42: 142
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.78    3.82 1.00e+00 1.00e+00 1.46e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.34    4.86 1.30e+00 5.92e-01 1.40e+01
  angle model="   0" pdb=" C   TYR A  81 "
        model="   0" pdb=" N   THR A  82 "
        model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta    sigma   weight residual
     121.70  128.42   -6.72 1.80e+00 3.09e-01 1.40e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.42   -5.02 1.40e+00 5.10e-01 1.29e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.82    4.38 1.30e+00 5.92e-01 1.14e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.51: 976
       16.51 -    33.02: 40
       33.02 -    49.53: 10
       49.53 -    66.03: 4
       66.03 -    82.54: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.95   31.05     0      5.00e+00 4.00e-02 3.86e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.49   28.51     0      5.00e+00 4.00e-02 3.25e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.17   20.83     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.038: 70
       0.038 -    0.075: 42
       0.075 -    0.111: 38
       0.111 -    0.148: 22
       0.148 -    0.185: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.54e-01
  chirality model="   0" pdb=" CG  LEU A  53 "
            model="   0" pdb=" CB  LEU A  53 "
            model="   0" pdb=" CD1 LEU A  53 "
            model="   0" pdb=" CD2 LEU A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.89e-01
  chirality model="   0" pdb=" CA  PRO A   6 "
            model="   0" pdb=" N   PRO A   6 "
            model="   0" pdb=" C   PRO A   6 "
            model="   0" pdb=" CB  PRO A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.74e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.064 2.00e-02 2.50e+03   2.88e-02 2.49e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.055 2.00e-02 2.50e+03   2.18e-02 1.42e+01
        model="   0" pdb=" CG  TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.044 2.00e-02 2.50e+03   1.74e-02 9.06e+00
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 190
        2.23 -     2.82: 4578
        2.82 -     3.41: 5927
        3.41 -     4.01: 7346
        4.01 -     4.60: 11092
  Nonbonded interactions: 29133
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.633 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.695 1.850
  nonbonded model="   0" pdb=" O   TYR A  81 "
            model="   0" pdb=" H   THR A  83 "
     model   vdw
     1.728 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.758 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.781 1.850
  ... (remaining 29128 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.01, per 1000 atoms: 0.46
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (76.977, 43.383, 56.733, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'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)----------                  


  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU   24": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.07, per 1000 atoms: 0.48
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (53.829, 56.829, 47.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (65.194, 55.367, 42.527, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.00 seconds

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'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: 1.08
  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.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 87
        1.23 -     1.43: 384
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.58e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.50e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.386 -0.032 1.10e-02 8.26e+03 8.22e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.17e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.76e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.23 -   105.98: 83
      105.98 -   111.74: 2481
      111.74 -   117.49: 504
      117.49 -   123.25: 818
      123.25 -   129.01: 191
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.53    4.07 1.00e+00 1.00e+00 1.66e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.62    4.58 1.30e+00 5.92e-01 1.24e+01
  angle model="   0" pdb=" N   PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" CB  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     103.00  106.85   -3.85 1.10e+00 8.26e-01 1.23e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.16    3.44 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.01   -4.61 1.40e+00 5.10e-01 1.08e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 969
       17.27 -    34.54: 41
       34.54 -    51.81: 15
       51.81 -    69.07: 5
       69.07 -    86.34: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.74   40.26     0      5.00e+00 4.00e-02 6.48e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.69   26.31     0      5.00e+00 4.00e-02 2.77e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.042: 77
       0.042 -    0.083: 42
       0.083 -    0.124: 38
       0.124 -    0.165: 16
       0.165 -    0.206: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.060 2.00e-02 2.50e+03   2.57e-02 1.98e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.054 2.00e-02 2.50e+03   2.10e-02 1.32e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.051 2.00e-02 2.50e+03   1.98e-02 1.18e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 196
        2.22 -     2.81: 4530
        2.81 -     3.41: 5961
        3.41 -     4.00: 7404
        4.00 -     4.60: 11096
  Nonbonded interactions: 29187
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.625 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.649 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.694 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.778 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.790 1.850
  ... (remaining 29182 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   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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 137
        1.23 -     1.43: 338
        1.43 -     1.62: 656
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.34e+01
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.32e+01
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.31e+01
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.29e+01
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.28e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       95.11 -   102.80: 13
      102.80 -   110.49: 2170
      110.49 -   118.17: 984
      118.17 -   125.86: 883
      125.86 -   133.55: 27
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  101.38   12.52 1.80e+00 3.09e-01 4.84e+01
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  107.13    6.67 1.00e+00 1.00e+00 4.45e+01
  angle model="   0" pdb=" C   ASP A 110 "
        model="   0" pdb=" N   TYR A 111 "
        model="   0" pdb=" CA  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     121.70  133.55  -11.85 1.80e+00 3.09e-01 4.33e+01
  angle model="   0" pdb=" C   THR A  92 "
        model="   0" pdb=" N   LEU A  93 "
        model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta    sigma   weight residual
     121.70  110.79   10.91 1.80e+00 3.09e-01 3.67e+01
  angle model="   0" pdb=" CA  ASP A  95 "
        model="   0" pdb=" CB  ASP A  95 "
        model="   0" pdb=" CG  ASP A  95 "
      ideal   model   delta    sigma   weight residual
     112.60  106.70    5.90 1.00e+00 1.00e+00 3.48e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.52: 935
       13.52 -    27.04: 53
       27.04 -    40.55: 26
       40.55 -    54.07: 13
       54.07 -    67.59: 5
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   ILE A  51 "
           model="   0" pdb=" CA  ILE A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.52  -19.48     0      5.00e+00 4.00e-02 1.52e+01
  dihedral model="   0" pdb=" CA  GLY A  73 "
           model="   0" pdb=" C   GLY A  73 "
           model="   0" pdb=" N   ASP A  74 "
           model="   0" pdb=" CA  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.78  -17.22     0      5.00e+00 4.00e-02 1.19e+01
  dihedral model="   0" pdb=" C   LYS A  10 "
           model="   0" pdb=" N   LYS A  10 "
           model="   0" pdb=" CA  LYS A  10 "
           model="   0" pdb=" CB  LYS A  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.31   -8.29     0      2.50e+00 1.60e-01 1.10e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 117
       0.072 -    0.143: 42
       0.143 -    0.214: 9
       0.214 -    0.286: 5
       0.286 -    0.357: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.18e+00
  chirality model="   0" pdb=" CA  PRO A   6 "
            model="   0" pdb=" N   PRO A   6 "
            model="   0" pdb=" C   PRO A   6 "
            model="   0" pdb=" CB  PRO A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.36    0.36 2.00e-01 2.50e+01 3.17e+00
  chirality model="   0" pdb=" CA  TYR A 111 "
            model="   0" pdb=" N   TYR A 111 "
            model="   0" pdb=" C   TYR A 111 "
            model="   0" pdb=" CB  TYR A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.54e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "    0.065 5.00e-02 4.00e+02   9.93e-02 1.58e+01
        model="   0" pdb=" N   PRO A  54 "   -0.172 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "    0.054 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "    0.053 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.058 5.00e-02 4.00e+02   8.85e-02 1.25e+01
        model="   0" pdb=" N   PRO A   6 "    0.153 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.048 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.047 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  ILE A  71 "   -0.017 2.00e-02 2.50e+03   3.38e-02 1.14e+01
        model="   0" pdb=" C   ILE A  71 "    0.058 2.00e-02 2.50e+03
        model="   0" pdb=" O   ILE A  71 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" N   ASN A  72 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.12 -     1.82: 39
        1.82 -     2.51: 1887
        2.51 -     3.21: 7254
        3.21 -     3.90: 8079
        3.90 -     4.60: 12709
  Nonbonded interactions: 29968
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  78 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.121 2.270
  nonbonded model="   0" pdb="HD21 LEU A   2 "
            model="   0" pdb="HD12 ILE A   4 "
     model   vdw
     1.184 2.440
  nonbonded model="   0" pdb="HD23 LEU A   9 "
            model="   0" pdb="HD21 LEU A  26 "
     model   vdw
     1.205 2.440
  nonbonded model="   0" pdb="HG22 THR A  83 "
            model="   0" pdb=" H   GLU A  84 "
     model   vdw
     1.373 2.270
  nonbonded model="   0" pdb="HG22 THR A  82 "
            model="   0" pdb=" H   THR A  83 "
     model   vdw
     1.392 2.270
  ... (remaining 29963 not shown)

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

  Symmetric amino acids flipped
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU   16": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

  Time building chain proxies: 1.12, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (64.093, 75.371, 45.259, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A TYR  111": "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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.23, per 1000 atoms: 0.55
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (51.102, 62.011, 57.868, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.26, per 1000 atoms: 0.57
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.795, 68.048, 40.559, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Time building chain proxies: 1.03, per 1000 atoms: 0.46
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.946, 50.867, 77.528, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.21, per 1000 atoms: 0.55
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (55.913, 69.82, 56.473, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

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: 2217
  At special positions: 0
  Unit cell: (61.54, 59.421, 54.582, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (46.859, 54.624, 72.748, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  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.

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (48.146, 64.372, 55.696, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  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.

  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (45.18, 64.909, 51.555, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (66.565, 44.274, 49.779, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 121
        1.23 -     1.43: 350
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.08e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.90e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.83e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.21e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.93e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      101.08 -   106.73: 150
      106.73 -   112.37: 2540
      112.37 -   118.02: 411
      118.02 -   123.67: 851
      123.67 -   129.32: 125
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.16    4.44 1.00e+00 1.00e+00 1.97e+01
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  128.03   -6.33 1.80e+00 3.09e-01 1.24e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.32   -4.92 1.40e+00 5.10e-01 1.24e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.65    4.55 1.30e+00 5.92e-01 1.23e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.17    3.43 1.00e+00 1.00e+00 1.18e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.98: 973
       16.98 -    33.96: 42
       33.96 -    50.93: 12
       50.93 -    67.91: 3
       67.91 -    84.89: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.21   28.79     0      5.00e+00 4.00e-02 3.32e+01
  dihedral model="   0" pdb=" CA  HIS A 135 "
           model="   0" pdb=" C   HIS A 135 "
           model="   0" pdb=" N   HIS A 136 "
           model="   0" pdb=" CA  HIS A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.90   26.10     0      5.00e+00 4.00e-02 2.72e+01
  dihedral model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" C   HIS A 137 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.96   24.04     0      5.00e+00 4.00e-02 2.31e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 74
       0.041 -    0.082: 47
       0.082 -    0.123: 35
       0.123 -    0.164: 14
       0.164 -    0.205: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 135 "
            model="   0" pdb=" N   HIS A 135 "
            model="   0" pdb=" C   HIS A 135 "
            model="   0" pdb=" CB  HIS A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.81e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.92e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.055 2.00e-02 2.50e+03   2.17e-02 1.41e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.050 2.00e-02 2.50e+03   2.09e-02 1.31e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.052 2.00e-02 2.50e+03   2.04e-02 1.24e+01
        model="   0" pdb=" CG  TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.010 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 213
        2.24 -     2.83: 4673
        2.83 -     3.42: 5799
        3.42 -     4.01: 7225
        4.01 -     4.60: 10789
  Nonbonded interactions: 28699
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.653 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.701 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.717 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.743 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  84 "
            model="   0" pdb=" HG1 THR A  92 "
     model   vdw
     1.759 1.850
  ... (remaining 28694 not shown)

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

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 10
        1.23 -     1.42: 454
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.335 -0.014 1.00e-02 1.00e+04 2.06e+00
  bond model="   0" pdb=" C   HIS A 135 "
       model="   0" pdb=" N   HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.78e+00
  bond model="   0" pdb=" C   GLU A 123 "
       model="   0" pdb=" N   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.43e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.35e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.332 -0.011 1.00e-02 1.00e+04 1.27e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.46 -   106.61: 49
      106.61 -   112.76: 2723
      112.76 -   118.91: 435
      118.91 -   125.06: 828
      125.06 -   131.21: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
        model="   0" pdb=" NH2 ARG A  21 "
      ideal   model   delta    sigma   weight residual
     119.20  120.63   -1.43 9.00e-01 1.23e+00 2.54e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.73   -4.73 3.00e+00 1.11e-01 2.49e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.55   -4.55 3.00e+00 1.11e-01 2.30e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  104.45    4.55 3.00e+00 1.11e-01 2.30e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  104.49    4.51 3.00e+00 1.11e-01 2.26e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.86: 996
       15.86 -    31.72: 22
       31.72 -    47.58: 10
       47.58 -    63.44: 3
       63.44 -    79.30: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   LEU A   2 "
           model="   0" pdb=" CA  LEU A   2 "
           model="   0" pdb=" CB  LEU A   2 "
           model="   0" pdb=" CG  LEU A   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.48   55.48     3      1.50e+01 4.44e-03 9.35e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -100.70  -79.30     2      3.00e+01 1.11e-03 5.15e+00
  dihedral model="   0" pdb=" CA  ASP A  88 "
           model="   0" pdb=" CB  ASP A  88 "
           model="   0" pdb=" CG  ASP A  88 "
           model="   0" pdb=" OD1 ASP A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   32.73  -32.73     1      2.00e+01 2.50e-03 3.81e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 113
       0.026 -    0.052: 37
       0.052 -    0.077: 18
       0.077 -    0.103: 6
       0.103 -    0.129: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.81e-01
  chirality model="   0" pdb=" CA  ILE A  30 "
            model="   0" pdb=" N   ILE A  30 "
            model="   0" pdb=" C   ILE A  30 "
            model="   0" pdb=" CB  ILE A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.10 2.00e-01 2.50e+01 2.65e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.014 5.00e-02 4.00e+02   2.15e-02 7.38e-01
        model="   0" pdb=" N   PRO A   6 "   -0.037 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.011 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.012 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.006 2.00e-02 2.50e+03   4.85e-03 7.07e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "   -0.013 5.00e-02 4.00e+02   1.97e-02 6.19e-01
        model="   0" pdb=" N   PRO A  54 "    0.034 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "   -0.010 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 122
        2.17 -     2.78: 4599
        2.78 -     3.39: 5847
        3.39 -     3.99: 7481
        3.99 -     4.60: 11645
  Nonbonded interactions: 29694
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 LEU A   3 "
            model="   0" pdb="HD11 LEU A  53 "
     model   vdw
     1.563 2.440
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.717 2.270
  nonbonded model="   0" pdb=" OE1 GLU A  16 "
            model="   0" pdb=" H   GLU A  16 "
     model   vdw
     1.780 1.850
  nonbonded model="   0" pdb="HD12 ILE A  37 "
            model="   0" pdb="HD23 LEU A  61 "
     model   vdw
     1.781 2.440
  nonbonded model="   0" pdb="HG22 ILE A 122 "
            model="   0" pdb=" H   ALA A 124 "
     model   vdw
     1.784 2.270
  ... (remaining 29689 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'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: 1.17 seconds

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.25, per 1000 atoms: 0.56
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (45.353, 49.279, 46.396, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 121
        1.23 -     1.43: 350
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.354 -0.033 1.00e-02 1.00e+04 1.07e+01
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.18e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.21e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.385 -0.031 1.10e-02 8.26e+03 8.07e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.47e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.28 -   106.22: 104
      106.22 -   112.17: 2552
      112.17 -   118.12: 456
      118.12 -   124.07: 873
      124.07 -   130.02: 92
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  130.02   -8.32 1.80e+00 3.09e-01 2.14e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.15    4.45 1.00e+00 1.00e+00 1.98e+01
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  128.87   -7.17 1.80e+00 3.09e-01 1.59e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.53    4.67 1.30e+00 5.92e-01 1.29e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  119.02    3.58 1.00e+00 1.00e+00 1.28e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.83: 963
       16.83 -    33.66: 52
       33.66 -    50.49: 12
       50.49 -    67.32: 3
       67.32 -    84.15: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.91  -28.09     0      5.00e+00 4.00e-02 3.16e+01
  dihedral model="   0" pdb=" CA  LYS A 113 "
           model="   0" pdb=" C   LYS A 113 "
           model="   0" pdb=" N   PRO A 114 "
           model="   0" pdb=" CA  PRO A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.79   16.21     0      5.00e+00 4.00e-02 1.05e+01
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.08   15.92     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 74
       0.042 -    0.083: 40
       0.083 -    0.124: 40
       0.124 -    0.166: 16
       0.166 -    0.207: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.21e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.20e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.114 2.00e-02 2.50e+03   4.86e-02 7.09e+01
        model="   0" pdb=" CG  TYR A  81 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.095 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.023 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.074 2.00e-02 2.50e+03   3.27e-02 3.21e+01
        model="   0" pdb=" CG  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.067 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.051 2.00e-02 2.50e+03   2.05e-02 1.26e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 104
        2.13 -     2.75: 3923
        2.75 -     3.37: 6223
        3.37 -     3.98: 7564
        3.98 -     4.60: 11333
  Nonbonded interactions: 29147
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.514 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.747 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.765 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.781 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.787 1.850
  ... (remaining 29142 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: 2217
  At special positions: 0
  Unit cell: (45.122, 49.938, 74.261, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (42.748, 66.847, 60.735, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

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

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

  Time building geometry restraints manager: 1.09 seconds

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


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

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

  Time building geometry restraints manager: 0.77 seconds

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

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

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 85
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.51e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.14e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.385 -0.031 1.10e-02 8.26e+03 7.83e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.92e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" CD2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.65e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.56 -   106.95: 191
      106.95 -   113.34: 2613
      113.34 -   119.73: 507
      119.73 -   126.12: 745
      126.12 -   132.51: 21
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   ALA A 115 "
        model="   0" pdb=" N   ASP A 116 "
        model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta    sigma   weight residual
     121.70  132.25  -10.55 1.80e+00 3.09e-01 3.43e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.39    4.21 1.00e+00 1.00e+00 1.77e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.16   -3.56 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.29   -4.89 1.40e+00 5.10e-01 1.22e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.77    4.43 1.30e+00 5.92e-01 1.16e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 967
       17.10 -    34.19: 43
       34.19 -    51.29: 18
       51.29 -    68.38: 2
       68.38 -    85.48: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.24   29.76     0      5.00e+00 4.00e-02 3.54e+01
  dihedral model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" C   ASP A 116 "
           model="   0" pdb=" N   PRO A 117 "
           model="   0" pdb=" CA  PRO A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.75   29.25     0      5.00e+00 4.00e-02 3.42e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.92   27.08     0      5.00e+00 4.00e-02 2.93e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 73
       0.044 -    0.088: 54
       0.088 -    0.131: 33
       0.131 -    0.175: 11
       0.175 -    0.218: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  90 "
            model="   0" pdb=" N   SER A  90 "
            model="   0" pdb=" C   SER A  90 "
            model="   0" pdb=" CB  SER A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality model="   0" pdb=" CA  ASP A 118 "
            model="   0" pdb=" N   ASP A 118 "
            model="   0" pdb=" C   ASP A 118 "
            model="   0" pdb=" CB  ASP A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.081 2.00e-02 2.50e+03   3.58e-02 3.85e+01
        model="   0" pdb=" CG  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.065 2.00e-02 2.50e+03   2.56e-02 1.97e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.045 2.00e-02 2.50e+03   1.71e-02 8.81e+00
        model="   0" pdb=" CG  TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.02: 35
        2.02 -     2.67: 3023
        2.67 -     3.31: 6520
        3.31 -     3.96: 7732
        3.96 -     4.60: 11607
  Nonbonded interactions: 28917
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HG  SER A  90 "
     model   vdw
     1.379 1.850
  nonbonded model="   0" pdb=" O   ALA A 115 "
            model="   0" pdb=" HD3 PRO A 117 "
     model   vdw
     1.632 2.620
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.645 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.672 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.763 1.850
  ... (remaining 28912 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: 134
        1.23 -     1.43: 338
        1.43 -     1.62: 659
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" NE  ARG A 127 "
       model="   0" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.370 -0.044 1.10e-02 8.26e+03 1.61e+01
  bond model="   0" pdb=" NE  ARG A 129 "
       model="   0" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.369 -0.043 1.10e-02 8.26e+03 1.53e+01
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.45e+01
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.44e+01
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.39e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       93.96 -   102.05: 9
      102.05 -   110.13: 2078
      110.13 -   118.22: 1081
      118.22 -   126.30: 881
      126.30 -   134.38: 28
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  106.56    7.24 1.00e+00 1.00e+00 5.25e+01
  angle model="   0" pdb=" C   ASP A 110 "
        model="   0" pdb=" N   TYR A 111 "
        model="   0" pdb=" CA  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     121.70  134.38  -12.68 1.80e+00 3.09e-01 4.97e+01
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  103.50   10.40 1.80e+00 3.09e-01 3.34e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" CB  ASP A 118 "
        model="   0" pdb=" CG  ASP A 118 "
      ideal   model   delta    sigma   weight residual
     112.60  106.92    5.68 1.00e+00 1.00e+00 3.23e+01
  angle model="   0" pdb=" C   ILE A  78 "
        model="   0" pdb=" N   LYS A  79 "
        model="   0" pdb=" CA  LYS A  79 "
      ideal   model   delta    sigma   weight residual
     121.70  131.85  -10.15 1.80e+00 3.09e-01 3.18e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.50: 952
       16.50 -    33.00: 63
       33.00 -    49.50: 11
       49.50 -    66.01: 4
       66.01 -    82.51: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   ILE A  51 "
           model="   0" pdb=" CA  ILE A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.61  -18.39     0      5.00e+00 4.00e-02 1.35e+01
  dihedral model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.19    8.59     0      2.50e+00 1.60e-01 1.18e+01
  dihedral model="   0" pdb=" C   LEU A  93 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
           model="   0" pdb=" CB  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.03   -8.57     0      2.50e+00 1.60e-01 1.17e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 125
       0.096 -    0.192: 33
       0.192 -    0.288: 14
       0.288 -    0.384: 3
       0.384 -    0.480: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.77e+00
  chirality model="   0" pdb=" CA  PRO A   6 "
            model="   0" pdb=" N   PRO A   6 "
            model="   0" pdb=" C   PRO A   6 "
            model="   0" pdb=" CB  PRO A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.36    0.36 2.00e-01 2.50e+01 3.20e+00
  chirality model="   0" pdb=" CA  ILE A  37 "
            model="   0" pdb=" N   ILE A  37 "
            model="   0" pdb=" C   ILE A  37 "
            model="   0" pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.11    0.32 2.00e-01 2.50e+01 2.61e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.055 5.00e-02 4.00e+02   8.47e-02 1.15e+01
        model="   0" pdb=" N   PRO A   6 "    0.147 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.046 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.045 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LYS A 101 "    0.053 5.00e-02 4.00e+02   8.12e-02 1.05e+01
        model="   0" pdb=" N   PRO A 102 "   -0.140 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A 102 "    0.044 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A 102 "    0.043 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  ILE A  71 "    0.017 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        model="   0" pdb=" C   ILE A  71 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" O   ILE A  71 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" N   ASN A  72 "    0.019 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.87: 55
        1.87 -     2.56: 2295
        2.56 -     3.24: 7238
        3.24 -     3.92: 8023
        3.92 -     4.60: 12554
  Nonbonded interactions: 30165
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  78 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.193 2.270
  nonbonded model="   0" pdb="HD11 LEU A  93 "
            model="   0" pdb=" HB2 LEU A  99 "
     model   vdw
     1.214 2.440
  nonbonded model="   0" pdb=" HA  THR A  34 "
            model="   0" pdb="HD11 ILE A  37 "
     model   vdw
     1.324 2.440
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.352 2.270
  nonbonded model="   0" pdb=" H   ILE A  37 "
            model="   0" pdb="HD13 ILE A  37 "
     model   vdw
     1.381 2.270
  ... (remaining 30160 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, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'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: 1.12 seconds

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

  Time building chain proxies: 0.78, per 1000 atoms: 0.35
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (47.292, 52.325, 39.909, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.19 seconds

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 1.12 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: 1.24 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 461
        1.42 -     1.61: 670
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   GLU A 133 "
       model="   0" pdb=" N   HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.21e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.365  0.013 1.10e-02 8.26e+03 1.49e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.49e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.36e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.315  0.015 1.30e-02 5.92e+03 1.25e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.13 -   106.28: 46
      106.28 -   112.42: 2690
      112.42 -   118.57: 450
      118.57 -   124.72: 826
      124.72 -   130.86: 65
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.62    5.38 3.00e+00 1.11e-01 3.22e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.77    5.23 3.00e+00 1.11e-01 3.04e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.23   -5.23 3.00e+00 1.11e-01 3.04e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  114.06   -5.06 3.00e+00 1.11e-01 2.84e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  105.02    4.98 3.00e+00 1.11e-01 2.75e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 997
       17.32 -    34.65: 21
       34.65 -    51.97: 7
       51.97 -    69.30: 5
       69.30 -    86.62: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   79.81  -79.81     1      3.00e+01 1.11e-03 8.78e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -93.38  -86.62     2      3.00e+01 1.11e-03 5.31e+00
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   59.45  -59.45     1      3.00e+01 1.11e-03 5.25e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 101
       0.026 -    0.051: 41
       0.051 -    0.077: 24
       0.077 -    0.102: 9
       0.102 -    0.128: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.09e-01
  chirality model="   0" pdb=" CA  ASP A  44 "
            model="   0" pdb=" N   ASP A  44 "
            model="   0" pdb=" C   ASP A  44 "
            model="   0" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.41    0.10 2.00e-01 2.50e+01 2.32e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.09 2.00e-01 2.50e+01 2.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.017 5.00e-02 4.00e+02   2.51e-02 1.01e+00
        model="   0" pdb=" N   PRO A   6 "    0.043 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.014 2.00e-02 2.50e+03   5.75e-03 9.91e-01
        model="   0" pdb=" CG  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ASP A 116 "    0.015 5.00e-02 4.00e+02   2.33e-02 8.68e-01
        model="   0" pdb=" N   PRO A 117 "   -0.040 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A 117 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A 117 "    0.013 5.00e-02 4.00e+02
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 167
        2.20 -     2.80: 4650
        2.80 -     3.40: 6064
        3.40 -     4.00: 7684
        4.00 -     4.60: 11872
  Nonbonded interactions: 30437
  Sorted by model distance:
  nonbonded model="   0" pdb=" H   GLY A  87 "
            model="   0" pdb=" HB2 SER A  90 "
     model   vdw
     1.599 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.677 1.850
  nonbonded model="   0" pdb=" HE2 MET A   1 "
            model="   0" pdb="HD21 LEU A   3 "
     model   vdw
     1.686 2.440
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" O   ASP A  44 "
     model   vdw
     1.692 2.620
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.735 1.850
  ... (remaining 30432 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.98, per 1000 atoms: 0.44
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (52.97, 44.661, 42.321, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 108
        1.23 -     1.43: 363
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.78e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.08e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.69e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.58e+00
  bond model="   0" pdb=" C   ILE A  77 "
       model="   0" pdb=" N   ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.40e-02 5.10e+03 5.45e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.75 -   106.42: 124
      106.42 -   112.08: 2515
      112.08 -   117.75: 436
      117.75 -   123.42: 849
      123.42 -   129.08: 153
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.74    3.86 1.00e+00 1.00e+00 1.49e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.89    3.71 1.00e+00 1.00e+00 1.38e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.01   -3.41 1.00e+00 1.00e+00 1.16e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.08   -4.68 1.40e+00 5.10e-01 1.12e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.90    4.30 1.30e+00 5.92e-01 1.09e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 975
       17.10 -    34.20: 37
       34.20 -    51.31: 11
       51.31 -    68.41: 8
       68.41 -    85.51: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.48   26.52     0      5.00e+00 4.00e-02 2.81e+01
  dihedral model="   0" pdb=" CA  GLY A  87 "
           model="   0" pdb=" C   GLY A  87 "
           model="   0" pdb=" N   ASP A  88 "
           model="   0" pdb=" CA  ASP A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.25  -15.75     0      5.00e+00 4.00e-02 9.92e+00
  dihedral model="   0" pdb=" N   ASP A  36 "
           model="   0" pdb=" CA  ASP A  36 "
           model="   0" pdb=" CB  ASP A  36 "
           model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.57   54.57     3      1.50e+01 4.44e-03 9.29e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 73
       0.040 -    0.080: 43
       0.080 -    0.119: 35
       0.119 -    0.159: 23
       0.159 -    0.199: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  90 "
            model="   0" pdb=" N   SER A  90 "
            model="   0" pdb=" C   SER A  90 "
            model="   0" pdb=" CB  SER A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.89e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.72e-01
  chirality model="   0" pdb=" CG  LEU A  26 "
            model="   0" pdb=" CB  LEU A  26 "
            model="   0" pdb=" CD1 LEU A  26 "
            model="   0" pdb=" CD2 LEU A  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.20e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.051 2.00e-02 2.50e+03   2.25e-02 1.51e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.054 2.00e-02 2.50e+03   2.15e-02 1.38e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.055 2.00e-02 2.50e+03   2.13e-02 1.37e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 153
        2.20 -     2.80: 4345
        2.80 -     3.40: 6064
        3.40 -     4.00: 7428
        4.00 -     4.60: 11282
  Nonbonded interactions: 29272
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.597 1.850
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HG  SER A  90 "
     model   vdw
     1.661 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.705 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.710 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  49 "
            model="   0" pdb="HH12 ARG A 127 "
     model   vdw
     1.724 1.850
  ... (remaining 29267 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: 89
        1.23 -     1.43: 382
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.07e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.94e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.44e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.13e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.08e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.75 -   106.38: 115
      106.38 -   112.02: 2514
      112.02 -   117.65: 441
      117.65 -   123.28: 820
      123.28 -   128.92: 187
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.73    4.47 1.30e+00 5.92e-01 1.18e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.92   -4.52 1.40e+00 5.10e-01 1.04e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.46    3.14 1.00e+00 1.00e+00 9.84e+00
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  127.14    4.06 1.30e+00 5.92e-01 9.74e+00
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.70   -3.10 1.00e+00 1.00e+00 9.60e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 966
       17.07 -    34.14: 43
       34.14 -    51.21: 15
       51.21 -    68.28: 6
       68.28 -    85.35: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.78   22.22     0      5.00e+00 4.00e-02 1.97e+01
  dihedral model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" CB  HIS A 137 "
           model="   0" pdb=" CG  HIS A 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.39  -56.61     3      1.50e+01 4.44e-03 9.41e+00
  dihedral model="   0" pdb=" N   ASP A  36 "
           model="   0" pdb=" CA  ASP A  36 "
           model="   0" pdb=" CB  ASP A  36 "
           model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.14   51.14     3      1.50e+01 4.44e-03 8.98e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.042: 78
       0.042 -    0.084: 45
       0.084 -    0.125: 37
       0.125 -    0.166: 12
       0.166 -    0.207: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.18 2.00e-01 2.50e+01 7.68e-01
  chirality model="   0" pdb=" CG  LEU A  26 "
            model="   0" pdb=" CB  LEU A  26 "
            model="   0" pdb=" CD1 LEU A  26 "
            model="   0" pdb=" CD2 LEU A  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.27e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.064 2.00e-02 2.50e+03   2.75e-02 2.27e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.053 2.00e-02 2.50e+03   2.07e-02 1.29e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.047 2.00e-02 2.50e+03   1.84e-02 1.02e+01
        model="   0" pdb=" CG  TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.003 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 198
        2.22 -     2.82: 4499
        2.82 -     3.41: 5895
        3.41 -     4.01: 7323
        4.01 -     4.60: 10806
  Nonbonded interactions: 28721
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.630 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.720 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.754 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.780 1.850
  ... (remaining 28716 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: 62
        1.23 -     1.42: 409
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.355 -0.034 1.00e-02 1.00e+04 1.12e+01
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.74e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.385 -0.031 1.10e-02 8.26e+03 8.19e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.09e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.80e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   106.31: 110
      106.31 -   112.08: 2535
      112.08 -   117.85: 442
      117.85 -   123.62: 872
      123.62 -   129.39: 118
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.37    4.23 1.00e+00 1.00e+00 1.79e+01
  angle model="   0" pdb=" C   TYR A  89 "
        model="   0" pdb=" N   SER A  90 "
        model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta    sigma   weight residual
     121.70  128.54   -6.84 1.80e+00 3.09e-01 1.45e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.39   -4.99 1.40e+00 5.10e-01 1.27e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.23    3.37 1.00e+00 1.00e+00 1.14e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.84    4.36 1.30e+00 5.92e-01 1.13e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 964
       16.94 -    33.87: 45
       33.87 -    50.81: 15
       50.81 -    67.74: 6
       67.74 -    84.68: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.70  -17.30     0      5.00e+00 4.00e-02 1.20e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.14   15.86     0      5.00e+00 4.00e-02 1.01e+01
  dihedral model="   0" pdb=" N   LEU A   2 "
           model="   0" pdb=" CA  LEU A   2 "
           model="   0" pdb=" CB  LEU A   2 "
           model="   0" pdb=" CG  LEU A   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.15  -59.85     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 75
       0.043 -    0.085: 49
       0.085 -    0.127: 31
       0.127 -    0.169: 16
       0.169 -    0.212: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.056 2.00e-02 2.50e+03   2.33e-02 1.62e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.050 2.00e-02 2.50e+03   1.95e-02 1.14e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.049 2.00e-02 2.50e+03   1.92e-02 1.11e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 259
        2.27 -     2.85: 4981
        2.85 -     3.43: 5473
        3.43 -     4.02: 7163
        4.02 -     4.60: 10711
  Nonbonded interactions: 28587
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.687 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.745 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.787 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.820 1.850
  ... (remaining 28582 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: 1.16
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.29 seconds

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 463
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.024 1.40e-02 5.10e+03 2.84e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.26e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" CD2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.354  1.339  0.015 1.10e-02 8.26e+03 1.97e+00
  bond model="   0" pdb=" C   HIS A 137 "
       model="   0" pdb=" N   HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.52e+00
  bond model="   0" pdb=" C   TYR A  81 "
       model="   0" pdb=" N   THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.35e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       99.99 -   106.19: 43
      106.19 -   112.39: 2687
      112.39 -   118.59: 452
      118.59 -   124.78: 839
      124.78 -   130.98: 56
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.78    5.22 3.00e+00 1.11e-01 3.02e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.21   -5.21 3.00e+00 1.11e-01 3.02e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.84    5.16 3.00e+00 1.11e-01 2.96e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  105.24    4.76 3.00e+00 1.11e-01 2.52e+00
  angle model="   0" pdb=" N   VAL A  41 "
        model="   0" pdb=" CA  VAL A  41 "
        model="   0" pdb=" HA  VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.00  105.31    4.69 3.00e+00 1.11e-01 2.44e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 997
       17.37 -    34.74: 19
       34.74 -    52.11: 9
       52.11 -    69.48: 4
       69.48 -    86.85: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.46   85.46     1      3.00e+01 1.11e-03 9.82e+00
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   75.02  -75.02     1      3.00e+01 1.11e-03 7.91e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -93.15  -86.85     2      3.00e+01 1.11e-03 5.32e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 102
       0.027 -    0.053: 44
       0.053 -    0.079: 22
       0.079 -    0.106: 5
       0.106 -    0.132: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.11e-01
  chirality model="   0" pdb=" CA  VAL A 112 "
            model="   0" pdb=" N   VAL A 112 "
            model="   0" pdb=" C   VAL A 112 "
            model="   0" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.01e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.016 2.00e-02 2.50e+03   6.46e-03 1.25e+00
        model="   0" pdb=" CG  TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.016 5.00e-02 4.00e+02   2.44e-02 9.56e-01
        model="   0" pdb=" N   PRO A   6 "   -0.042 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "   -0.009 2.00e-02 2.50e+03   7.76e-03 9.04e-01
        model="   0" pdb=" CD  GLN A  66 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.01 -     1.73: 4
        1.73 -     2.45: 1203
        2.45 -     3.16: 7031
        3.16 -     3.88: 8414
        3.88 -     4.60: 13573
  Nonbonded interactions: 30225
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE1 TYR A  68 "
            model="   0" pdb=" HH  TYR A  81 "
     model   vdw
     1.012 2.100
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.545 1.850
  nonbonded model="   0" pdb=" O   LYS A  85 "
            model="   0" pdb=" HZ3 LYS A 101 "
     model   vdw
     1.611 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.715 1.850
  nonbonded model="   0" pdb="HD21 LEU A  39 "
            model="   0" pdb=" HE2 LYS A  85 "
     model   vdw
     1.758 2.440
  ... (remaining 30220 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: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 seconds

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'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: 1.20 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: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (76.96, 51.438, 43.295, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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


  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 1
        1.22 -     1.42: 462
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.298  0.031 1.40e-02 5.10e+03 4.77e+00
  bond model="   0" pdb=" C   PRO A 102 "
       model="   0" pdb=" N   ASP A 103 "
    ideal  model  delta    sigma   weight residual
    1.329  1.302  0.027 1.40e-02 5.10e+03 3.83e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.302  0.027 1.40e-02 5.10e+03 3.75e+00
  bond model="   0" pdb=" C   SER A  98 "
       model="   0" pdb=" N   LEU A  99 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.024 1.40e-02 5.10e+03 2.97e+00
  bond model="   0" pdb=" C   THR A  20 "
       model="   0" pdb=" N   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.40e-02 5.10e+03 2.62e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.58 -   106.65: 58
      106.65 -   112.73: 2699
      112.73 -   118.80: 439
      118.80 -   124.87: 827
      124.87 -   130.95: 54
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.77    5.23 3.00e+00 1.11e-01 3.04e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.81    5.19 3.00e+00 1.11e-01 2.99e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.01   -5.01 3.00e+00 1.11e-01 2.79e+00
  angle model="   0" pdb=" C   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  104.17    4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.73   -4.73 3.00e+00 1.11e-01 2.49e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 996
       17.90 -    35.80: 18
       35.80 -    53.69: 12
       53.69 -    71.59: 3
       71.59 -    89.49: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.49  -89.49     1      3.00e+01 1.11e-03 1.06e+01
  dihedral model="   0" pdb=" CB  GLU A 123 "
           model="   0" pdb=" CG  GLU A 123 "
           model="   0" pdb=" CD  GLU A 123 "
           model="   0" pdb=" OE1 GLU A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -73.51   73.51     1      3.00e+01 1.11e-03 7.64e+00
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   61.72  -61.72     1      3.00e+01 1.11e-03 5.61e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 101
       0.026 -    0.051: 41
       0.051 -    0.077: 19
       0.077 -    0.102: 11
       0.102 -    0.128: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.09e-01
  chirality model="   0" pdb=" CA  ASP A  44 "
            model="   0" pdb=" N   ASP A  44 "
            model="   0" pdb=" C   ASP A  44 "
            model="   0" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.03e-01
  chirality model="   0" pdb=" CA  ILE A  71 "
            model="   0" pdb=" N   ILE A  71 "
            model="   0" pdb=" C   ILE A  71 "
            model="   0" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.10 2.00e-01 2.50e+01 2.70e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.017 5.00e-02 4.00e+02   2.62e-02 1.10e+00
        model="   0" pdb=" N   PRO A   6 "    0.045 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.015 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.014 2.00e-02 2.50e+03   5.75e-03 9.91e-01
        model="   0" pdb=" CG  TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  LEU A   3 "   -0.004 2.00e-02 2.50e+03   7.21e-03 5.20e-01
        model="   0" pdb=" C   LEU A   3 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" O   LEU A   3 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" N   ILE A   4 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 33
        2.00 -     2.65: 3033
        2.65 -     3.30: 6781
        3.30 -     3.95: 8204
        3.95 -     4.60: 12620
  Nonbonded interactions: 30671
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 TYR A  89 "
            model="   0" pdb=" HB3 LYS A 101 "
     model   vdw
     1.354 2.440
  nonbonded model="   0" pdb=" HE2 MET A   1 "
            model="   0" pdb="HD21 LEU A   3 "
     model   vdw
     1.396 2.440
  nonbonded model="   0" pdb="HG21 THR A  82 "
            model="   0" pdb=" O   THR A  92 "
     model   vdw
     1.553 2.620
  nonbonded model="   0" pdb=" O   TYR A  89 "
            model="   0" pdb=" H   LYS A 101 "
     model   vdw
     1.558 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.558 1.850
  ... (remaining 30666 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 138
        1.23 -     1.43: 338
        1.43 -     1.62: 655
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" NE  ARG A 129 "
       model="   0" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.369 -0.043 1.10e-02 8.26e+03 1.53e+01
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.41e+01
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.38e+01
  bond model="   0" pdb=" NE  ARG A 127 "
       model="   0" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.366 -0.040 1.10e-02 8.26e+03 1.32e+01
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.31e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       94.95 -   102.77: 13
      102.77 -   110.60: 2204
      110.60 -   118.43: 963
      118.43 -   126.26: 870
      126.26 -   134.09: 27
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  100.71   13.19 1.80e+00 3.09e-01 5.37e+01
  angle model="   0" pdb=" C   GLU A  49 "
        model="   0" pdb=" N   TYR A  50 "
        model="   0" pdb=" CA  TYR A  50 "
      ideal   model   delta    sigma   weight residual
     121.70  134.09  -12.39 1.80e+00 3.09e-01 4.74e+01
  angle model="   0" pdb=" CA  ASN A  72 "
        model="   0" pdb=" CB  ASN A  72 "
        model="   0" pdb=" CG  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     112.60  105.87    6.73 1.00e+00 1.00e+00 4.53e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" CB  ASP A 118 "
        model="   0" pdb=" CG  ASP A 118 "
      ideal   model   delta    sigma   weight residual
     112.60  106.19    6.41 1.00e+00 1.00e+00 4.11e+01
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  107.75    6.05 1.00e+00 1.00e+00 3.66e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 946
       17.02 -    34.04: 65
       34.04 -    51.07: 15
       51.07 -    68.09: 5
       68.09 -    85.11: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.17   10.57     0      2.50e+00 1.60e-01 1.79e+01
  dihedral model="   0" pdb=" C   LYS A  10 "
           model="   0" pdb=" N   LYS A  10 "
           model="   0" pdb=" CA  LYS A  10 "
           model="   0" pdb=" CB  LYS A  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.16  -10.44     0      2.50e+00 1.60e-01 1.74e+01
  dihedral model="   0" pdb=" CA  ASP A  95 "
           model="   0" pdb=" C   ASP A  95 "
           model="   0" pdb=" N   GLY A  96 "
           model="   0" pdb=" CA  GLY A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.19  -19.81     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 115
       0.097 -    0.193: 41
       0.193 -    0.290: 12
       0.290 -    0.386: 5
       0.386 -    0.483: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.82e+00
  chirality model="   0" pdb=" CA  PRO A   6 "
            model="   0" pdb=" N   PRO A   6 "
            model="   0" pdb=" C   PRO A   6 "
            model="   0" pdb=" CB  PRO A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.25    0.47 2.00e-01 2.50e+01 5.54e+00
  chirality model="   0" pdb=" CA  LYS A  27 "
            model="   0" pdb=" N   LYS A  27 "
            model="   0" pdb=" C   LYS A  27 "
            model="   0" pdb=" CB  LYS A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.54e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ILE A  51 "    0.079 5.00e-02 4.00e+02   1.21e-01 2.34e+01
        model="   0" pdb=" N   PRO A  52 "   -0.209 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  52 "    0.064 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  52 "    0.066 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.066 5.00e-02 4.00e+02   1.01e-01 1.62e+01
        model="   0" pdb=" N   PRO A   6 "    0.174 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.055 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.053 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LYS A 113 "    0.055 5.00e-02 4.00e+02   8.42e-02 1.13e+01
        model="   0" pdb=" N   PRO A 114 "   -0.146 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A 114 "    0.045 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A 114 "    0.045 5.00e-02 4.00e+02
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.87: 48
        1.87 -     2.55: 2285
        2.55 -     3.24: 7187
        3.24 -     3.92: 8023
        3.92 -     4.60: 12449
  Nonbonded interactions: 29992
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  78 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.191 2.270
  nonbonded model="   0" pdb="HG12 ILE A 131 "
            model="   0" pdb=" HB2 HIS A 134 "
     model   vdw
     1.288 2.440
  nonbonded model="   0" pdb=" H   LYS A  79 "
            model="   0" pdb=" HD3 LYS A  79 "
     model   vdw
     1.373 2.270
  nonbonded model="   0" pdb=" HB3 LYS A  10 "
            model="   0" pdb=" HD3 LYS A  19 "
     model   vdw
     1.404 2.440
  nonbonded model="   0" pdb="HD22 LEU A   2 "
            model="   0" pdb=" HG  LEU A  61 "
     model   vdw
     1.429 2.440
  ... (remaining 29987 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: 3
        1.23 -     1.42: 460
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.296  0.033 1.40e-02 5.10e+03 5.49e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.301  0.028 1.40e-02 5.10e+03 3.94e+00
  bond model="   0" pdb=" C   THR A  20 "
       model="   0" pdb=" N   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.329  1.303  0.026 1.40e-02 5.10e+03 3.41e+00
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.024 1.40e-02 5.10e+03 2.90e+00
  bond model="   0" pdb=" C   ILE A 108 "
       model="   0" pdb=" N   LYS A 109 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.40e-02 5.10e+03 2.72e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       99.86 -   106.07: 43
      106.07 -   112.28: 2681
      112.28 -   118.49: 459
      118.49 -   124.70: 825
      124.70 -   130.91: 69
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.27   -5.27 3.00e+00 1.11e-01 3.09e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.78    5.22 3.00e+00 1.11e-01 3.03e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.89    5.11 3.00e+00 1.11e-01 2.90e+00
  angle model="   0" pdb=" C   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  104.06    4.94 3.00e+00 1.11e-01 2.72e+00
  angle model="   0" pdb=" N   VAL A  41 "
        model="   0" pdb=" CA  VAL A  41 "
        model="   0" pdb=" HA  VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.00  105.09    4.91 3.00e+00 1.11e-01 2.68e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.72: 987
       15.72 -    31.45: 21
       31.45 -    47.17: 15
       47.17 -    62.89: 6
       62.89 -    78.62: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   GLU A  55 "
           model="   0" pdb=" CA  GLU A  55 "
           model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.45   55.45     3      1.50e+01 4.44e-03 9.35e+00
  dihedral model="   0" pdb=" CB  GLU A 133 "
           model="   0" pdb=" CG  GLU A 133 "
           model="   0" pdb=" CD  GLU A 133 "
           model="   0" pdb=" OE1 GLU A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -73.29   73.29     1      3.00e+01 1.11e-03 7.60e+00
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -69.24   69.24     1      3.00e+01 1.11e-03 6.89e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 104
       0.027 -    0.054: 40
       0.054 -    0.080: 22
       0.080 -    0.107: 7
       0.107 -    0.134: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.38e-01
  chirality model="   0" pdb=" CA  ASP A  44 "
            model="   0" pdb=" N   ASP A  44 "
            model="   0" pdb=" C   ASP A  44 "
            model="   0" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.95e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.017 2.00e-02 2.50e+03   6.91e-03 1.43e+00
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.017 5.00e-02 4.00e+02   2.58e-02 1.06e+00
        model="   0" pdb=" N   PRO A   6 "   -0.045 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "   -0.008 2.00e-02 2.50e+03   6.58e-03 6.49e-01
        model="   0" pdb=" CD  GLN A  66 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 102
        2.12 -     2.74: 4197
        2.74 -     3.36: 6223
        3.36 -     3.98: 7892
        3.98 -     4.60: 12114
  Nonbonded interactions: 30528
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE2 MET A   1 "
            model="   0" pdb="HD21 LEU A   3 "
     model   vdw
     1.503 2.440
  nonbonded model="   0" pdb="HG21 THR A  82 "
            model="   0" pdb=" O   THR A  92 "
     model   vdw
     1.729 2.620
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HB2 SER A  90 "
     model   vdw
     1.733 2.620
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HG  SER A  90 "
     model   vdw
     1.759 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.825 1.850
  ... (remaining 30523 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: 2217
  At special positions: 0
  Unit cell: (63.976, 43.891, 60.889, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

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


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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.07 seconds

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


============================== 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: 1.03
  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: 10
        1.23 -     1.42: 454
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   ILE A 108 "
       model="   0" pdb=" N   LYS A 109 "
    ideal  model  delta    sigma   weight residual
    1.329  1.304  0.025 1.40e-02 5.10e+03 3.22e+00
  bond model="   0" pdb=" C   PRO A 114 "
       model="   0" pdb=" N   ALA A 115 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.58e+00
  bond model="   0" pdb=" C   VAL A  41 "
       model="   0" pdb=" N   GLY A  42 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.43e+00
  bond model="   0" pdb=" C   THR A  20 "
       model="   0" pdb=" N   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.20e+00
  bond model="   0" pdb=" C   SER A  11 "
       model="   0" pdb=" N   TYR A  12 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.11e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.25 -   106.39: 56
      106.39 -   112.52: 2681
      112.52 -   118.65: 451
      118.65 -   124.78: 829
      124.78 -   130.91: 60
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.62    5.38 3.00e+00 1.11e-01 3.22e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.68    5.32 3.00e+00 1.11e-01 3.14e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.24   -5.24 3.00e+00 1.11e-01 3.06e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  114.06   -5.06 3.00e+00 1.11e-01 2.84e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  104.99    5.01 3.00e+00 1.11e-01 2.79e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 986
       16.92 -    33.85: 24
       33.85 -    50.77: 13
       50.77 -    67.69: 5
       67.69 -    84.61: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.61  -84.61     1      3.00e+01 1.11e-03 9.67e+00
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   75.07  -75.07     1      3.00e+01 1.11e-03 7.92e+00
  dihedral model="   0" pdb=" CB  ARG A 129 "
           model="   0" pdb=" CG  ARG A 129 "
           model="   0" pdb=" CD  ARG A 129 "
           model="   0" pdb=" NE  ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.84  -41.16     3      1.50e+01 4.44e-03 7.36e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 85
       0.023 -    0.047: 47
       0.047 -    0.070: 26
       0.070 -    0.094: 12
       0.094 -    0.117: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  VAL A 112 "
            model="   0" pdb=" N   VAL A 112 "
            model="   0" pdb=" C   VAL A 112 "
            model="   0" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.43e-01
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.25e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.48e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.015 2.00e-02 2.50e+03   6.57e-03 1.29e+00
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.017 5.00e-02 4.00e+02   2.63e-02 1.11e+00
        model="   0" pdb=" N   PRO A   6 "    0.046 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.015 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 105 "    0.016 2.00e-02 2.50e+03   5.94e-03 1.06e+00
        model="   0" pdb=" CG  TYR A 105 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 105 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 105 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 105 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 105 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 105 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 105 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 105 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 105 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 105 "    0.000 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        0.97 -     1.70: 9
        1.70 -     2.42: 1121
        2.42 -     3.15: 7110
        3.15 -     3.87: 8793
        3.87 -     4.60: 14218
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 31251
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ2 LYS A 101 "
            model="   0" pdb=" HE1 HIS A 135 "
     model   vdw
     0.972 2.100
  nonbonded model="   0" pdb=" OE2 GLU A  84 "
            model="   0" pdb=" HD1 TYR A  89 "
     model   vdw
     1.205 2.450
  nonbonded model="   0" pdb=" O   LYS A  40 "
            model="   0" pdb=" HD2 ARG A 127 "
     model   vdw
     1.333 2.620
  nonbonded model="   0" pdb=" HZ  PHE A  67 "
            model="   0" pdb=" HE1 TYR A  91 "
     model   vdw
     1.523 2.100
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.589 1.850
  ... (remaining 31246 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: 136
        1.23 -     1.43: 339
        1.43 -     1.62: 656
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" NE  ARG A  21 "
       model="   0" pdb=" CZ  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.39e+01
  bond model="   0" pdb=" NE  ARG A  58 "
       model="   0" pdb=" CZ  ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.38e+01
  bond model="   0" pdb=" NE  ARG A 127 "
       model="   0" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.37e+01
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.33e+01
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.32e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       95.85 -   103.29: 22
      103.29 -   110.73: 2257
      110.73 -   118.16: 889
      118.16 -   125.60: 872
      125.60 -   133.04: 37
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  102.43   11.47 1.80e+00 3.09e-01 4.06e+01
  angle model="   0" pdb=" C   ASP A 110 "
        model="   0" pdb=" N   TYR A 111 "
        model="   0" pdb=" CA  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     121.70  133.04  -11.34 1.80e+00 3.09e-01 3.97e+01
  angle model="   0" pdb=" CA  ASP A   7 "
        model="   0" pdb=" CB  ASP A   7 "
        model="   0" pdb=" CG  ASP A   7 "
      ideal   model   delta    sigma   weight residual
     112.60  106.31    6.29 1.00e+00 1.00e+00 3.95e+01
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  107.52    6.28 1.00e+00 1.00e+00 3.95e+01
  angle model="   0" pdb=" C   GLU A  49 "
        model="   0" pdb=" N   TYR A  50 "
        model="   0" pdb=" CA  TYR A  50 "
      ideal   model   delta    sigma   weight residual
     121.70  132.58  -10.88 1.80e+00 3.09e-01 3.65e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 962
       17.04 -    34.07: 56
       34.07 -    51.11: 7
       51.11 -    68.14: 4
       68.14 -    85.18: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   ASN A  72 "
           model="   0" pdb=" C   ASN A  72 "
           model="   0" pdb=" CA  ASN A  72 "
           model="   0" pdb=" CB  ASN A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.33  -10.53     0      2.50e+00 1.60e-01 1.78e+01
  dihedral model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.39    9.79     0      2.50e+00 1.60e-01 1.53e+01
  dihedral model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.24   -9.44     0      2.50e+00 1.60e-01 1.43e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 134
       0.098 -    0.196: 25
       0.196 -    0.294: 12
       0.294 -    0.392: 2
       0.392 -    0.489: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASN A  72 "
            model="   0" pdb=" N   ASN A  72 "
            model="   0" pdb=" C   ASN A  72 "
            model="   0" pdb=" CB  ASN A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 5.99e+00
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.48 2.00e-01 2.50e+01 5.65e+00
  chirality model="   0" pdb=" CA  PRO A   6 "
            model="   0" pdb=" N   PRO A   6 "
            model="   0" pdb=" C   PRO A   6 "
            model="   0" pdb=" CB  PRO A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.32    0.39 2.00e-01 2.50e+01 3.89e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ILE A  51 "    0.075 5.00e-02 4.00e+02   1.14e-01 2.08e+01
        model="   0" pdb=" N   PRO A  52 "   -0.197 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  52 "    0.060 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  52 "    0.062 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  ASN A  72 "   -0.019 2.00e-02 2.50e+03   3.73e-02 1.39e+01
        model="   0" pdb=" C   ASN A  72 "    0.065 2.00e-02 2.50e+03
        model="   0" pdb=" O   ASN A  72 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" N   GLY A  73 "   -0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.057 5.00e-02 4.00e+02   8.72e-02 1.22e+01
        model="   0" pdb=" N   PRO A   6 "    0.151 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.048 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.21 -     1.88: 55
        1.88 -     2.56: 2353
        2.56 -     3.24: 7155
        3.24 -     3.92: 7987
        3.92 -     4.60: 12572
  Nonbonded interactions: 30122
  Sorted by model distance:
  nonbonded model="   0" pdb="HD23 LEU A   9 "
            model="   0" pdb="HD12 LEU A  26 "
     model   vdw
     1.206 2.440
  nonbonded model="   0" pdb="HG22 ILE A  78 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.245 2.270
  nonbonded model="   0" pdb=" HB3 LEU A   2 "
            model="   0" pdb="HG22 ILE A   4 "
     model   vdw
     1.299 2.440
  nonbonded model="   0" pdb="HG22 THR A  82 "
            model="   0" pdb=" H   THR A  83 "
     model   vdw
     1.385 2.270
  nonbonded model="   0" pdb=" HA  MET A   1 "
            model="   0" pdb=" HE2 MET A   1 "
     model   vdw
     1.398 2.440
  ... (remaining 30117 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 462
        1.42 -     1.61: 669
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.463  0.028 2.10e-02 2.27e+03 1.75e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" CD2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.354  1.341  0.013 1.10e-02 8.26e+03 1.47e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.365  0.013 1.10e-02 8.26e+03 1.42e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.37e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.315  0.015 1.30e-02 5.92e+03 1.30e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.14 -   106.38: 49
      106.38 -   112.62: 2700
      112.62 -   118.85: 446
      118.85 -   125.09: 840
      125.09 -   131.33: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.35   -5.35 3.00e+00 1.11e-01 3.19e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.81    5.19 3.00e+00 1.11e-01 3.00e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  105.00    5.00 3.00e+00 1.11e-01 2.78e+00
  angle model="   0" pdb=" C   LEU A   3 "
        model="   0" pdb=" N   ILE A   4 "
        model="   0" pdb=" CA  ILE A   4 "
      ideal   model   delta    sigma   weight residual
     121.70  124.65   -2.95 1.80e+00 3.09e-01 2.68e+00
  angle model="   0" pdb=" C   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  104.22    4.78 3.00e+00 1.11e-01 2.54e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 988
       16.92 -    33.83: 25
       33.83 -    50.75: 9
       50.75 -    67.66: 6
       67.66 -    84.58: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.58   84.58     1      3.00e+01 1.11e-03 9.66e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -98.62  -81.38     2      3.00e+01 1.11e-03 5.21e+00
  dihedral model="   0" pdb=" CA  PRO A 117 "
           model="   0" pdb=" C   PRO A 117 "
           model="   0" pdb=" N   ASP A 118 "
           model="   0" pdb=" CA  ASP A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  168.70   11.30     0      5.00e+00 4.00e-02 5.11e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 113
       0.028 -    0.055: 33
       0.055 -    0.082: 19
       0.082 -    0.110: 10
       0.110 -    0.137: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.72e-01
  chirality model="   0" pdb=" CA  ILE A  71 "
            model="   0" pdb=" N   ILE A  71 "
            model="   0" pdb=" C   ILE A  71 "
            model="   0" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.96e-01
  chirality model="   0" pdb=" CA  ASP A  44 "
            model="   0" pdb=" N   ASP A  44 "
            model="   0" pdb=" C   ASP A  44 "
            model="   0" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.41    0.10 2.00e-01 2.50e+01 2.75e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.018 2.00e-02 2.50e+03   6.90e-03 1.43e+00
        model="   0" pdb=" CG  TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.017 5.00e-02 4.00e+02   2.61e-02 1.09e+00
        model="   0" pdb=" N   PRO A   6 "   -0.045 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.015 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "   -0.013 5.00e-02 4.00e+02   1.94e-02 6.02e-01
        model="   0" pdb=" N   PRO A  54 "    0.034 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "   -0.010 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.41 -     2.05: 40
        2.05 -     2.69: 3310
        2.69 -     3.32: 6458
        3.32 -     3.96: 7894
        3.96 -     4.60: 12053
  Nonbonded interactions: 29755
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.409 1.850
  nonbonded model="   0" pdb=" HB3 TYR A  89 "
            model="   0" pdb=" HB3 LYS A 101 "
     model   vdw
     1.555 2.440
  nonbonded model="   0" pdb=" O   TYR A  89 "
            model="   0" pdb=" H   LYS A 101 "
     model   vdw
     1.637 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.662 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.792 1.850
  ... (remaining 29750 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'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: 0.96
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 11
        1.23 -     1.42: 453
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.362  0.016 1.10e-02 8.26e+03 2.13e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.88e+00
  bond model="   0" pdb=" N   MET A   1 "
       model="   0" pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.491  1.463  0.028 2.10e-02 2.27e+03 1.73e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.314  0.016 1.30e-02 5.92e+03 1.54e+00
  bond model="   0" pdb=" C   THR A  20 "
       model="   0" pdb=" N   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.015 1.40e-02 5.10e+03 1.18e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.46 -   106.60: 64
      106.60 -   112.74: 2689
      112.74 -   118.88: 443
      118.88 -   125.03: 835
      125.03 -   131.17: 46
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.69    5.31 3.00e+00 1.11e-01 3.13e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.23   -5.23 3.00e+00 1.11e-01 3.03e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.81    5.19 3.00e+00 1.11e-01 3.00e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  104.95    5.05 3.00e+00 1.11e-01 2.84e+00
  angle model="   0" pdb=" C   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  104.11    4.89 3.00e+00 1.11e-01 2.66e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 998
       17.53 -    35.06: 19
       35.06 -    52.58: 9
       52.58 -    70.11: 4
       70.11 -    87.64: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.84   83.84     1      3.00e+01 1.11e-03 9.52e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -92.36  -87.64     2      3.00e+01 1.11e-03 5.32e+00
  dihedral model="   0" pdb=" CA  TYR A  12 "
           model="   0" pdb=" C   TYR A  12 "
           model="   0" pdb=" N   SER A  13 "
           model="   0" pdb=" CA  SER A  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -168.69  -11.31     0      5.00e+00 4.00e-02 5.12e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 96
       0.026 -    0.053: 43
       0.053 -    0.079: 21
       0.079 -    0.106: 12
       0.106 -    0.132: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality model="   0" pdb=" CA  ILE A  77 "
            model="   0" pdb=" N   ILE A  77 "
            model="   0" pdb=" C   ILE A  77 "
            model="   0" pdb=" CB  ILE A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.52e-01
  chirality model="   0" pdb=" CA  VAL A 112 "
            model="   0" pdb=" N   VAL A 112 "
            model="   0" pdb=" C   VAL A 112 "
            model="   0" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.24e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.016 2.00e-02 2.50e+03   6.42e-03 1.24e+00
        model="   0" pdb=" CG  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.016 5.00e-02 4.00e+02   2.49e-02 9.94e-01
        model="   0" pdb=" N   PRO A   6 "    0.043 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "    0.007 2.00e-02 2.50e+03   6.14e-03 5.65e-01
        model="   0" pdb=" CD  GLN A  66 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "    0.009 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.00 -     1.72: 8
        1.72 -     2.44: 1190
        2.44 -     3.16: 7134
        3.16 -     3.88: 8722
        3.88 -     4.60: 14040
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 31094
  Sorted by model distance:
  nonbonded model="   0" pdb="HG21 THR A  82 "
            model="   0" pdb=" O   THR A  92 "
     model   vdw
     0.996 2.620
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.381 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.523 1.850
  nonbonded model="   0" pdb=" HE1 TYR A  89 "
            model="   0" pdb=" HE1 HIS A 135 "
     model   vdw
     1.626 2.100
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.633 1.850
  ... (remaining 31089 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.61, per 1000 atoms: 0.28
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (42.36, 60.909, 71.438, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (47.415, 44.04, 81.691, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'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  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

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

  Time building geometry restraints manager: 1.13 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: 4
        1.23 -     1.42: 460
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   LYS A  85 "
       model="   0" pdb=" N   ILE A  86 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.62e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" ND1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.378  1.364  0.014 1.10e-02 8.26e+03 1.58e+00
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.50e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.315  0.015 1.30e-02 5.92e+03 1.32e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.366  0.012 1.10e-02 8.26e+03 1.28e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.06 -   106.30: 52
      106.30 -   112.54: 2678
      112.54 -   118.77: 461
      118.77 -   125.01: 841
      125.01 -   131.25: 45
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CG  LYS A  85 "
        model="   0" pdb=" CD  LYS A  85 "
        model="   0" pdb=" CE  LYS A  85 "
      ideal   model   delta    sigma   weight residual
     111.30  115.54   -4.24 2.30e+00 1.89e-01 3.40e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.48   -5.48 3.00e+00 1.11e-01 3.33e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.80    5.20 3.00e+00 1.11e-01 3.00e+00
  angle model="   0" pdb=" CD  LYS A  85 "
        model="   0" pdb=" CE  LYS A  85 "
        model="   0" pdb=" NZ  LYS A  85 "
      ideal   model   delta    sigma   weight residual
     111.90  117.40   -5.50 3.20e+00 9.77e-02 2.96e+00
  angle model="   0" pdb=" C   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  103.96    5.04 3.00e+00 1.11e-01 2.82e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 991
       17.78 -    35.55: 22
       35.55 -    53.33: 11
       53.33 -    71.11: 6
       71.11 -    88.88: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CG  LYS A  85 "
           model="   0" pdb=" CD  LYS A  85 "
           model="   0" pdb=" CE  LYS A  85 "
           model="   0" pdb=" NZ  LYS A  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    8.35   51.65     3      1.50e+01 4.44e-03 9.04e+00
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   74.51  -74.51     1      3.00e+01 1.11e-03 7.82e+00
  dihedral model="   0" pdb=" CB  GLU A  24 "
           model="   0" pdb=" CG  GLU A  24 "
           model="   0" pdb=" CD  GLU A  24 "
           model="   0" pdb=" OE1 GLU A  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   63.55  -63.55     1      3.00e+01 1.11e-03 5.92e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 102
       0.027 -    0.054: 39
       0.054 -    0.081: 28
       0.081 -    0.107: 6
       0.107 -    0.134: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.50e-01
  chirality model="   0" pdb=" CA  ASP A  44 "
            model="   0" pdb=" N   ASP A  44 "
            model="   0" pdb=" C   ASP A  44 "
            model="   0" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.83e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.10 2.00e-01 2.50e+01 2.66e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.015 2.00e-02 2.50e+03   6.05e-03 1.10e+00
        model="   0" pdb=" CG  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.016 5.00e-02 4.00e+02   2.44e-02 9.49e-01
        model="   0" pdb=" N   PRO A   6 "   -0.042 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "    0.007 2.00e-02 2.50e+03   5.91e-03 5.24e-01
        model="   0" pdb=" CD  GLN A  66 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "    0.008 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.37 -     2.02: 45
        2.02 -     2.66: 3043
        2.66 -     3.31: 6731
        3.31 -     3.95: 8284
        3.95 -     4.60: 12694
  Nonbonded interactions: 30797
  Sorted by model distance:
  nonbonded model="   0" pdb=" OH  TYR A  68 "
            model="   0" pdb=" HZ1 LYS A 125 "
     model   vdw
     1.371 1.850
  nonbonded model="   0" pdb="HD22 LEU A  39 "
            model="   0" pdb=" O   LEU A 119 "
     model   vdw
     1.559 2.620
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.660 1.850
  nonbonded model="   0" pdb=" O   VAL A  41 "
            model="   0" pdb=" H   LYS A 113 "
     model   vdw
     1.669 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  55 "
            model="   0" pdb="HH12 ARG A  58 "
     model   vdw
     1.693 1.850
  ... (remaining 30792 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: 0.80
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.88 seconds

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

  Time building chain proxies: 1.21, per 1000 atoms: 0.55
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (80.136, 44.915, 46.377, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (59.499, 64.415, 49.947, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 57
        1.23 -     1.42: 414
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.70e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.24e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.88e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.84e+00
  bond model="   0" pdb=" C   MET A   1 "
       model="   0" pdb=" N   LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.365 -0.036 1.40e-02 5.10e+03 6.56e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      101.21 -   106.78: 173
      106.78 -   112.35: 2505
      112.35 -   117.91: 408
      117.91 -   123.48: 844
      123.48 -   129.05: 147
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.38    4.22 1.00e+00 1.00e+00 1.78e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.82   -4.22 1.00e+00 1.00e+00 1.78e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.11    3.49 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.09   -3.49 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.86    4.34 1.30e+00 5.92e-01 1.12e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 969
       17.69 -    35.37: 42
       35.37 -    53.06: 17
       53.06 -    70.75: 3
       70.75 -    88.43: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.06   31.94     0      5.00e+00 4.00e-02 4.08e+01
  dihedral model="   0" pdb=" CA  VAL A 112 "
           model="   0" pdb=" C   VAL A 112 "
           model="   0" pdb=" N   LYS A 113 "
           model="   0" pdb=" CA  LYS A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.09   16.91     0      5.00e+00 4.00e-02 1.14e+01
  dihedral model="   0" pdb=" CA  LYS A 113 "
           model="   0" pdb=" C   LYS A 113 "
           model="   0" pdb=" N   PRO A 114 "
           model="   0" pdb=" CA  PRO A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 76
       0.047 -    0.094: 50
       0.094 -    0.141: 41
       0.141 -    0.188: 7
       0.188 -    0.235: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.27e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.056 2.00e-02 2.50e+03   2.39e-02 1.72e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.057 2.00e-02 2.50e+03   2.31e-02 1.60e+01
        model="   0" pdb=" CG  TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.018 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        model="   0" pdb=" CG  ASP A  36 "    0.062 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 228
        2.24 -     2.83: 4671
        2.83 -     3.42: 5817
        3.42 -     4.01: 7335
        4.01 -     4.60: 10978
  Nonbonded interactions: 29029
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.649 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.714 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A 109 "
            model="   0" pdb=" OD1 ASP A 110 "
     model   vdw
     1.758 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.791 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.797 1.850
  ... (remaining 29024 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'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.

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

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

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

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 108
        1.23 -     1.43: 363
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.78e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.39e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.25e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.12e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.29e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.11 -   105.91: 75
      105.91 -   111.72: 2483
      111.72 -   117.52: 508
      117.52 -   123.33: 837
      123.33 -   129.13: 174
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.85    3.75 1.00e+00 1.00e+00 1.41e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.90    3.70 1.00e+00 1.00e+00 1.37e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.13    3.47 1.00e+00 1.00e+00 1.21e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.13   -4.73 1.40e+00 5.10e-01 1.14e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.82    4.38 1.30e+00 5.92e-01 1.13e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.66: 959
       15.66 -    31.32: 51
       31.32 -    46.98: 14
       46.98 -    62.64: 7
       62.64 -    78.30: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.64   26.36     0      5.00e+00 4.00e-02 2.78e+01
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.48   24.52     0      5.00e+00 4.00e-02 2.40e+01
  dihedral model="   0" pdb=" N   LYS A 125 "
           model="   0" pdb=" CA  LYS A 125 "
           model="   0" pdb=" CB  LYS A 125 "
           model="   0" pdb=" CG  LYS A 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.32  -53.68     3      1.50e+01 4.44e-03 9.22e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.037: 68
       0.037 -    0.073: 45
       0.073 -    0.108: 36
       0.108 -    0.144: 21
       0.144 -    0.180: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.06e-01
  chirality model="   0" pdb=" CA  PRO A  54 "
            model="   0" pdb=" N   PRO A  54 "
            model="   0" pdb=" C   PRO A  54 "
            model="   0" pdb=" CB  PRO A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.34e-01
  chirality model="   0" pdb=" CG  LEU A  53 "
            model="   0" pdb=" CB  LEU A  53 "
            model="   0" pdb=" CD1 LEU A  53 "
            model="   0" pdb=" CD2 LEU A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.32e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.058 2.00e-02 2.50e+03   2.31e-02 1.59e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.056 2.00e-02 2.50e+03   2.15e-02 1.39e+01
        model="   0" pdb=" CG  TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.050 2.00e-02 2.50e+03   2.13e-02 1.36e+01
        model="   0" pdb=" CG  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 207
        2.23 -     2.83: 4655
        2.83 -     3.42: 5871
        3.42 -     4.01: 7370
        4.01 -     4.60: 10981
  Nonbonded interactions: 29084
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.642 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  49 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.677 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.702 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.737 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.764 1.850
  ... (remaining 29079 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (55.81, 57.804, 53.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  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.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 101
        1.23 -     1.43: 370
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.33e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.58e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.87e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.64e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.378 -0.024 1.10e-02 8.26e+03 4.94e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       99.89 -   105.70: 64
      105.70 -   111.52: 2415
      111.52 -   117.33: 576
      117.33 -   123.15: 813
      123.15 -   128.96: 209
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.06    3.54 1.00e+00 1.00e+00 1.25e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.85    4.35 1.30e+00 5.92e-01 1.12e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.93    4.27 1.30e+00 5.92e-01 1.08e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.96   -4.56 1.40e+00 5.10e-01 1.06e+01
  angle model="   0" pdb=" N   PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" CB  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     103.00  106.46   -3.46 1.10e+00 8.26e-01 9.88e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 974
       17.73 -    35.45: 41
       35.45 -    53.17: 12
       53.17 -    70.90: 4
       70.90 -    88.62: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.39   35.61     0      5.00e+00 4.00e-02 5.07e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.63   19.37     0      5.00e+00 4.00e-02 1.50e+01
  dihedral model="   0" pdb=" N   ASP A  36 "
           model="   0" pdb=" CA  ASP A  36 "
           model="   0" pdb=" CB  ASP A  36 "
           model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.37  -57.63     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.039: 68
       0.039 -    0.077: 45
       0.077 -    0.115: 36
       0.115 -    0.153: 23
       0.153 -    0.192: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.18e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.77e-01
  chirality model="   0" pdb=" CG  LEU A  53 "
            model="   0" pdb=" CB  LEU A  53 "
            model="   0" pdb=" CD1 LEU A  53 "
            model="   0" pdb=" CD2 LEU A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.21e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.052 2.00e-02 2.50e+03   2.39e-02 1.71e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.058 2.00e-02 2.50e+03   2.30e-02 1.59e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.053 2.00e-02 2.50e+03   2.07e-02 1.28e+01
        model="   0" pdb=" CG  TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 154
        2.20 -     2.80: 4379
        2.80 -     3.40: 6061
        3.40 -     4.00: 7399
        4.00 -     4.60: 11148
  Nonbonded interactions: 29141
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.598 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.682 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.767 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.768 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.772 1.850
  ... (remaining 29136 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.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 107
        1.23 -     1.43: 364
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.68e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.13e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.04e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.50e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.00e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.36 -   106.21: 100
      106.21 -   112.06: 2531
      112.06 -   117.91: 458
      117.91 -   123.76: 874
      123.76 -   129.61: 114
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     121.70  129.61   -7.91 1.80e+00 3.09e-01 1.93e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.81    3.79 1.00e+00 1.00e+00 1.44e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.63    4.57 1.30e+00 5.92e-01 1.23e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.65    4.55 1.30e+00 5.92e-01 1.22e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.06   -3.46 1.00e+00 1.00e+00 1.20e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 966
       17.01 -    34.01: 44
       34.01 -    51.02: 16
       51.02 -    68.02: 4
       68.02 -    85.03: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.89  -22.11     0      5.00e+00 4.00e-02 1.96e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.00   20.00     0      5.00e+00 4.00e-02 1.60e+01
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.30   16.70     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 75
       0.040 -    0.080: 43
       0.080 -    0.120: 33
       0.120 -    0.160: 18
       0.160 -    0.199: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.95e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.05e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.86e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.063 2.00e-02 2.50e+03   2.76e-02 2.28e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.067 2.00e-02 2.50e+03   2.65e-02 2.10e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.056 2.00e-02 2.50e+03   2.18e-02 1.42e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 144
        2.19 -     2.79: 4296
        2.79 -     3.39: 5935
        3.39 -     4.00: 7203
        4.00 -     4.60: 10929
  Nonbonded interactions: 28507
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.587 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.622 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.733 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.762 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.765 1.850
  ... (remaining 28502 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: 0.88
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.24: 127
        1.24 -     1.43: 344
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.01e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.44e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.15e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 6.07e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.05e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.73 -   106.46: 126
      106.46 -   112.19: 2528
      112.19 -   117.92: 436
      117.92 -   123.64: 864
      123.64 -   129.37: 123
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.78    3.82 1.00e+00 1.00e+00 1.46e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.28   -3.68 1.00e+00 1.00e+00 1.35e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.37   -4.97 1.40e+00 5.10e-01 1.26e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.05   -3.45 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.73    4.47 1.30e+00 5.92e-01 1.18e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 974
       16.96 -    33.91: 42
       33.91 -    50.87: 11
       50.87 -    67.82: 4
       67.82 -    84.78: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" CB  HIS A 137 "
           model="   0" pdb=" CG  HIS A 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.24   51.24     3      1.50e+01 4.44e-03 8.99e+00
  dihedral model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
           model="   0" pdb=" CB  HIS A 139 "
           model="   0" pdb=" CG  HIS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -104.76   44.76     3      1.50e+01 4.44e-03 8.05e+00
  dihedral model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" CB  HIS A 138 "
           model="   0" pdb=" CG  HIS A 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -103.75   43.75     3      1.50e+01 4.44e-03 7.87e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 74
       0.038 -    0.075: 42
       0.075 -    0.113: 31
       0.113 -    0.150: 24
       0.150 -    0.188: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.82e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.28e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.073 2.00e-02 2.50e+03   3.16e-02 3.00e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.061 2.00e-02 2.50e+03   2.42e-02 1.76e+01
        model="   0" pdb=" CG  TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.051 2.00e-02 2.50e+03   1.96e-02 1.15e+01
        model="   0" pdb=" CG  TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.000 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 271
        2.27 -     2.85: 5068
        2.85 -     3.43: 5517
        3.43 -     4.02: 7308
        4.02 -     4.60: 10796
  Nonbonded interactions: 28960
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.688 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.695 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.739 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.754 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.759 1.850
  ... (remaining 28955 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: 0.96
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 83
        1.23 -     1.43: 388
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.43e+00
  bond model="   0" pdb=" ND1 HIS A 134 "
       model="   0" pdb=" CE1 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.00e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.83e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.10e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" CD2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.04e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.26 -   106.11: 99
      106.11 -   111.97: 2517
      111.97 -   117.82: 472
      117.82 -   123.68: 859
      123.68 -   129.53: 130
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.69    3.91 1.00e+00 1.00e+00 1.53e+01
  angle model="   0" pdb=" CB  HIS A 138 "
        model="   0" pdb=" CG  HIS A 138 "
        model="   0" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  126.42    4.78 1.30e+00 5.92e-01 1.35e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.93    3.67 1.00e+00 1.00e+00 1.35e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.53   -5.13 1.40e+00 5.10e-01 1.34e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.45    4.75 1.30e+00 5.92e-01 1.33e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 977
       17.11 -    34.22: 33
       34.22 -    51.33: 16
       51.33 -    68.43: 5
       68.43 -    85.54: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.19   20.81     0      5.00e+00 4.00e-02 1.73e+01
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.67   20.33     0      5.00e+00 4.00e-02 1.65e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.15   15.85     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 64
       0.041 -    0.082: 53
       0.082 -    0.123: 34
       0.123 -    0.164: 19
       0.164 -    0.205: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.79e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.057 2.00e-02 2.50e+03   2.41e-02 1.75e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.060 2.00e-02 2.50e+03   2.37e-02 1.68e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 "   -0.036 2.00e-02 2.50e+03   2.16e-02 9.30e+00
        model="   0" pdb=" CG  HIS A 139 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 58
        2.09 -     2.71: 3566
        2.71 -     3.34: 6110
        3.34 -     3.97: 7433
        3.97 -     4.60: 11088
  Nonbonded interactions: 28255
  Sorted by model distance:
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.457 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.539 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.698 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.785 1.850
  ... (remaining 28250 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      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: 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, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 100
        1.23 -     1.43: 371
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.353 -0.032 1.00e-02 1.00e+04 1.01e+01
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 9.80e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.06e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 5.82e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.67e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.79 -   106.44: 122
      106.44 -   112.08: 2524
      112.08 -   117.73: 440
      117.73 -   123.38: 825
      123.38 -   129.02: 166
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.60    4.00 1.00e+00 1.00e+00 1.60e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.77    4.43 1.30e+00 5.92e-01 1.16e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.02   -4.62 1.40e+00 5.10e-01 1.09e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.95    4.25 1.30e+00 5.92e-01 1.07e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.82   -3.22 1.00e+00 1.00e+00 1.03e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 964
       16.99 -    33.98: 46
       33.98 -    50.97: 16
       50.97 -    67.96: 4
       67.96 -    84.95: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.69   26.31     0      5.00e+00 4.00e-02 2.77e+01
  dihedral model="   0" pdb=" CA  LYS A 113 "
           model="   0" pdb=" C   LYS A 113 "
           model="   0" pdb=" N   PRO A 114 "
           model="   0" pdb=" CA  PRO A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.78   15.22     0      5.00e+00 4.00e-02 9.27e+00
  dihedral model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
           model="   0" pdb=" CB  HIS A 139 "
           model="   0" pdb=" CG  HIS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.27   53.27     3      1.50e+01 4.44e-03 9.19e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 75
       0.041 -    0.081: 49
       0.081 -    0.122: 30
       0.122 -    0.162: 19
       0.162 -    0.203: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.73e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.69e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.245 2.00e-02 2.50e+03   1.08e-01 3.52e+02
        model="   0" pdb=" CG  TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.220 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.086 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.092 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.064 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.056 2.00e-02 2.50e+03   2.12e-02 1.35e+01
        model="   0" pdb=" CG  TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.043 2.00e-02 2.50e+03   1.91e-02 1.09e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 157
        2.19 -     2.79: 4329
        2.79 -     3.39: 6152
        3.39 -     4.00: 7470
        4.00 -     4.60: 11267
  Nonbonded interactions: 29375
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.582 2.440
  nonbonded model="   0" pdb=" HZ  PHE A  67 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.613 2.100
  nonbonded model="   0" pdb=" HH  TYR A  81 "
            model="   0" pdb=" CE1 TYR A  91 "
     model   vdw
     1.667 2.800
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.667 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.696 1.850
  ... (remaining 29370 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.042 (Z=  3.091)
  Mean delta:    0.012 (Z=  0.673)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.004 (Z=  0.002)
  Max. delta:    6.725 (Z=  3.819)
  Mean delta:    1.627 (Z=  0.887)

                      ----------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   148.95    31.05  5.00e+00  3.86e+01   6.2*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   151.49    28.51  5.00e+00  3.25e+01   5.7*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   159.17    20.83  5.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.003
  Max. delta:   82.543
  Mean delta:   11.460

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.185
  Mean delta:    0.074

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.058
  Mean delta:    0.011

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.042   2241  Z= 0.479
    Angle     :  1.557   6.725   4077  Z= 0.675
    Chirality :  0.074   0.185    176
    Planarity :  0.008   0.058    326
    Dihedral  : 10.595  82.543    768
    Min Nonbonded Distance : 1.633
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  2.92 %
      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 : 0.76 %
  
  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:  0.18 (0.72), residues: 137
    helix:  0.14 (0.49), residues: 92
    sheet: -0.71 (1.70), residues: 10
    loop :  0.87 (1.31), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.021   0.005   PHE A  45 
   TYR   0.064   0.011   TYR A  50 
   ARG   0.041   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.013   0.005   PHE A  67 
   TYR   0.054   0.013   TYR A  50 
   ARG   0.006   0.002   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   2.92 %
                favored =  94.16 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   2.71
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.56
  MolProbity score      =   1.45

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.95, per 1000 atoms: 0.43
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (46.402, 47.987, 49.734, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (66.811, 55.665, 51.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.040 (Z=  3.095)
  Mean delta:    0.012 (Z=  0.629)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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=  0.000)
  Max. delta:    6.740 (Z=  4.070)
  Mean delta:    1.594 (Z=  0.871)

                      ----------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   139.74    40.26  5.00e+00  6.48e+01   8.1*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   153.69    26.31  5.00e+00  2.77e+01   5.3*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   157.63    22.37  5.00e+00  2.00e+01   4.5*sigma

  Min. delta:    0.085
  Max. delta:   86.342
  Mean delta:   13.273

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.206
  Mean delta:    0.077

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.041
  Mean delta:    0.010

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2241  Z= 0.448
    Angle     :  1.543   6.740   4077  Z= 0.666
    Chirality :  0.077   0.206    176
    Planarity :  0.007   0.032    326
    Dihedral  : 11.587  86.342    768
    Min Nonbonded Distance : 1.625
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  0.73 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.03 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  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:  0.16 (0.71), residues: 137
    helix:  0.02 (0.50), residues: 89
    sheet: -0.88 (1.65), residues: 10
    loop :  1.15 (1.20), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.060   0.011   TYR A  50 
   ARG   0.036   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.012   0.004   PHE A  67 
   TYR   0.049   0.013   TYR A  50 
   ARG   0.003   0.001   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   3.65 %
                favored =  95.62 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.54
  MolProbity score      =   1.86

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

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


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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.055 (Z=  3.660)
  Mean delta:    0.018 (Z=  0.994)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   101.38    12.52  1.80e+00  4.84e+01   7.0*sigma
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   107.13     6.67  1.00e+00  4.45e+01   6.7*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   133.55   -11.85  1.80e+00  4.33e+01   6.6*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   110.79    10.91  1.80e+00  3.67e+01   6.1*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   106.70     5.90  1.00e+00  3.48e+01   5.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   106.79     5.81  1.00e+00  3.37e+01   5.8*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   107.41     5.19  1.00e+00  2.69e+01   5.2*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   130.98    -9.28  1.80e+00  2.66e+01   5.2*sigma
   A   7  ASP  CA
   A   7  ASP  CB
   A   7  ASP  CG        112.60   107.50     5.10  1.00e+00  2.60e+01   5.1*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   109.29     7.61  1.50e+00  2.57e+01   5.1*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   104.90     9.00  1.80e+00  2.50e+01   5.0*sigma
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        121.70   130.62    -8.92  1.80e+00  2.46e+01   5.0*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   107.69     4.91  1.00e+00  2.41e+01   4.9*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   107.77     4.83  1.00e+00  2.34e+01   4.8*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   130.32    -8.62  1.80e+00  2.30e+01   4.8*sigma
   A  29  ASP  CA
   A  29  ASP  CB
   A  29  ASP  CG        112.60   107.81     4.79  1.00e+00  2.29e+01   4.8*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   107.89     4.71  1.00e+00  2.22e+01   4.7*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   107.94     4.66  1.00e+00  2.17e+01   4.7*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   129.80    -8.10  1.80e+00  2.02e+01   4.5*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.50     4.50  1.00e+00  2.02e+01   4.5*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.52     4.48  1.00e+00  2.00e+01   4.5*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.53     4.47  1.00e+00  2.00e+01   4.5*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.55     4.45  1.00e+00  1.98e+01   4.5*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.58     4.42  1.00e+00  1.95e+01   4.4*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.60     4.40  1.00e+00  1.93e+01   4.4*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.66     4.34  1.00e+00  1.88e+01   4.3*sigma
   A   3  LEU  C
   A   4  ILE  N
   A   4  ILE  CA        121.70   129.33    -7.63  1.80e+00  1.80e+01   4.2*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   108.41     4.19  1.00e+00  1.76e+01   4.2*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   108.52     4.08  1.00e+00  1.66e+01   4.1*sigma
   A 103  ASP  C
   A 104  VAL  N
   A 104  VAL  CA        121.70   128.94    -7.24  1.80e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   12.520 (Z=  6.956)
  Mean delta:    2.247 (Z=  1.309)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   67.589
  Mean delta:   12.580

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.357
  Mean delta:    0.095

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.055   2241  Z= 0.708
    Angle     :  2.002  12.520   4077  Z= 0.938
    Chirality :  0.095   0.357    176
    Planarity :  0.012   0.099    326
    Dihedral  : 11.611  67.589    768
    Min Nonbonded Distance : 1.121
  
  Molprobity Statistics.
    All-atom Clashscore : 82.54
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  : 11.68 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  6.45 %
      Favored  : 90.32 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.97 (0.61), residues: 137
    helix:  0.26 (0.55), residues: 69
    sheet:  None (None), residues: 0
    loop : -3.16 (0.55), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.005   0.001   PHE A  15 
   TYR   0.009   0.002   TYR A  12 
   ARG   0.014   0.005   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 137 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.008   0.002   TYR A 111 
   ARG   0.005   0.002   ARG A  58 

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

   A  72  ASN
   A 100  GLN

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

  Ramachandran outliers =   0.00 %
                favored =  88.32 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =  82.54
  RMS(bonds)            =   0.0132
  RMS(angles)           =   2.00
  MolProbity score      =   3.36

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

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


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  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 disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

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

  Time building geometry restraints manager: 1.19 seconds

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


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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 97
        1.23 -     1.43: 374
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.09e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.57e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.42e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.25e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.95e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.62 -   106.39: 126
      106.39 -   112.16: 2521
      112.16 -   117.93: 459
      117.93 -   123.71: 847
      123.71 -   129.48: 124
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.49    4.11 1.00e+00 1.00e+00 1.69e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.48   -5.08 1.40e+00 5.10e-01 1.32e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.54    4.66 1.30e+00 5.92e-01 1.28e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.13   -3.53 1.00e+00 1.00e+00 1.25e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.71    4.49 1.30e+00 5.92e-01 1.19e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 965
       17.20 -    34.39: 49
       34.39 -    51.59: 12
       51.59 -    68.78: 4
       68.78 -    85.98: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.52   28.48     0      5.00e+00 4.00e-02 3.24e+01
  dihedral model="   0" pdb=" CA  HIS A 135 "
           model="   0" pdb=" C   HIS A 135 "
           model="   0" pdb=" N   HIS A 136 "
           model="   0" pdb=" CA  HIS A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.94   28.06     0      5.00e+00 4.00e-02 3.15e+01
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.43   27.57     0      5.00e+00 4.00e-02 3.04e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.041: 73
       0.041 -    0.082: 42
       0.082 -    0.122: 43
       0.122 -    0.163: 16
       0.163 -    0.203: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality model="   0" pdb=" CA  SER A  90 "
            model="   0" pdb=" N   SER A  90 "
            model="   0" pdb=" C   SER A  90 "
            model="   0" pdb=" CB  SER A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.27e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.45e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.061 2.00e-02 2.50e+03   2.44e-02 1.78e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.056 2.00e-02 2.50e+03   2.23e-02 1.49e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.048 2.00e-02 2.50e+03   1.94e-02 1.13e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.003 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.27: 266
        2.27 -     2.85: 5027
        2.85 -     3.43: 5530
        3.43 -     4.02: 7140
        4.02 -     4.60: 10826
  Nonbonded interactions: 28789
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.683 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.707 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.720 1.850
  nonbonded model="   0" pdb=" HA  ILE A  77 "
            model="   0" pdb=" OG1 THR A  82 "
     model   vdw
     1.728 2.620
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.734 1.850
  ... (remaining 28784 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: 13
        1.23 -     1.42: 451
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.364  0.014 1.10e-02 8.26e+03 1.58e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.26e+00
  bond model="   0" pdb=" C   ASP A  47 "
       model="   0" pdb=" N   ALA A  48 "
    ideal  model  delta    sigma   weight residual
    1.329  1.345 -0.016 1.40e-02 5.10e+03 1.24e+00
  bond model="   0" pdb=" C   PRO A 102 "
       model="   0" pdb=" N   ASP A 103 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.015 1.40e-02 5.10e+03 1.09e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" ND1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.378  1.367  0.011 1.10e-02 8.26e+03 1.09e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.44 -   106.64: 59
      106.64 -   112.84: 2703
      112.84 -   119.03: 441
      119.03 -   125.23: 832
      125.23 -   131.43: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.46    5.54 3.00e+00 1.11e-01 3.41e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.28   -5.28 3.00e+00 1.11e-01 3.10e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.80    5.20 3.00e+00 1.11e-01 3.00e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.97   -4.97 3.00e+00 1.11e-01 2.74e+00
  angle model="   0" pdb=" N   VAL A  41 "
        model="   0" pdb=" CA  VAL A  41 "
        model="   0" pdb=" HA  VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.00  105.08    4.92 3.00e+00 1.11e-01 2.68e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 981
       15.94 -    31.87: 30
       31.87 -    47.81: 16
       47.81 -    63.75: 3
       63.75 -    79.68: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   GLU A  55 "
           model="   0" pdb=" CA  GLU A  55 "
           model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.98  -57.02     3      1.50e+01 4.44e-03 9.42e+00
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   67.79  -67.79     1      3.00e+01 1.11e-03 6.63e+00
  dihedral model="   0" pdb=" CA  ASP A  74 "
           model="   0" pdb=" CB  ASP A  74 "
           model="   0" pdb=" CG  ASP A  74 "
           model="   0" pdb=" OD1 ASP A  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -71.97   41.97     1      2.00e+01 2.50e-03 6.16e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.027: 104
       0.027 -    0.054: 37
       0.054 -    0.080: 25
       0.080 -    0.107: 8
       0.107 -    0.133: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  chirality model="   0" pdb=" CA  VAL A 112 "
            model="   0" pdb=" N   VAL A 112 "
            model="   0" pdb=" C   VAL A 112 "
            model="   0" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.02e-01
  chirality model="   0" pdb=" CA  ASP A  44 "
            model="   0" pdb=" N   ASP A  44 "
            model="   0" pdb=" C   ASP A  44 "
            model="   0" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.78e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.017 5.00e-02 4.00e+02   2.56e-02 1.05e+00
        model="   0" pdb=" N   PRO A   6 "   -0.044 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.012 2.00e-02 2.50e+03   5.29e-03 8.39e-01
        model="   0" pdb=" CG  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "   -0.007 2.00e-02 2.50e+03   6.19e-03 5.75e-01
        model="   0" pdb=" CD  GLN A  66 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.26 -     1.93: 29
        1.93 -     2.60: 2384
        2.60 -     3.26: 7121
        3.26 -     3.93: 8442
        3.93 -     4.60: 13405
  Nonbonded interactions: 31381
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LEU A  39 "
            model="   0" pdb=" HD2 ARG A 127 "
     model   vdw
     1.261 2.620
  nonbonded model="   0" pdb=" HE2 MET A   1 "
            model="   0" pdb="HD21 LEU A   3 "
     model   vdw
     1.361 2.440
  nonbonded model="   0" pdb=" HH  TYR A  91 "
            model="   0" pdb=" NE2 HIS A 135 "
     model   vdw
     1.376 2.600
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.385 1.850
  nonbonded model="   0" pdb="HG21 ILE A  86 "
            model="   0" pdb="HD11 LEU A 132 "
     model   vdw
     1.484 2.440
  ... (remaining 31376 not shown)

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

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


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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.040 (Z=  2.841)
  Mean delta:    0.012 (Z=  0.654)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    5.990 (Z=  3.442)
  Mean delta:    1.586 (Z=  0.868)

                      ----------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   157.78    22.22  5.00e+00  1.97e+01   4.4*sigma

  Min. delta:    0.022
  Max. delta:   85.354
  Mean delta:   12.595

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.207
  Mean delta:    0.075

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2241  Z= 0.466
    Angle     :  1.534   5.990   4077  Z= 0.664
    Chirality :  0.075   0.207    176
    Planarity :  0.008   0.040    326
    Dihedral  : 11.715  85.354    768
    Min Nonbonded Distance : 1.630
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.92 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  3.23 %
      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:  0.22 (0.68), residues: 137
    helix: -0.05 (0.49), residues: 90
    sheet: -1.29 (1.52), residues: 10
    loop :  1.72 (1.11), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.064   0.010   TYR A  50 
   ARG   0.037   0.011   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.052   0.012   TYR A  50 
   ARG   0.005   0.002   ARG A  21 

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

   A  66  GLN

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  1.434)
  Mean delta:    0.005 (Z=  0.263)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.190 (Z=  1.593)
  Mean delta:    0.687 (Z=  0.340)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.010
  Max. delta:   79.303
  Mean delta:    7.906

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.129
  Mean delta:    0.035

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.021
  Mean delta:    0.003

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.022   2241  Z= 0.187
    Angle     :  1.062   4.733   4077  Z= 0.386
    Chirality :  0.035   0.129    176
    Planarity :  0.002   0.021    326
    Dihedral  :  8.193  79.303    768
    Min Nonbonded Distance : 1.563
  
  Molprobity Statistics.
    All-atom Clashscore : 6.77
    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:  0.44 (0.69), residues: 137
    helix:  0.26 (0.56), residues: 81
    sheet: -1.12 (1.49), residues: 10
    loop :  1.10 (0.89), residues: 46
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.007   0.002   PHE A  67 
   TYR   0.009   0.003   TYR A  91 
   ARG   0.007   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.004   0.002   PHE A  67 
   TYR   0.005   0.002   TYR A  12 
   ARG   0.001   0.000   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   6.77
  RMS(bonds)            =   0.0033
  RMS(angles)           =   1.06
  MolProbity score      =   1.37

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  96.35 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   2.71
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.53
  MolProbity score      =   1.30

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.87, per 1000 atoms: 0.39
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (76.963, 43.611, 45.753, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.843)
  Mean delta:    0.012 (Z=  0.609)

                        ----------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:    0.001 (Z=  0.001)
  Max. delta:    6.497 (Z=  4.442)
  Mean delta:    1.600 (Z=  0.879)

                      ----------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   151.21    28.79  5.00e+00  3.32e+01   5.8*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   153.90    26.10  5.00e+00  2.72e+01   5.2*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   155.96    24.04  5.00e+00  2.31e+01   4.8*sigma

  Min. delta:    0.022
  Max. delta:   84.890
  Mean delta:   11.992

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.205
  Mean delta:    0.079

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.042
  Mean delta:    0.010

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2241  Z= 0.433
    Angle     :  1.539   6.497   4077  Z= 0.669
    Chirality :  0.079   0.205    176
    Planarity :  0.008   0.034    326
    Dihedral  : 10.908  84.890    768
    Min Nonbonded Distance : 1.653
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.84 %
      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:  0.04 (0.71), residues: 137
    helix:  0.00 (0.51), residues: 87
    sheet: -1.38 (1.49), residues: 10
    loop :  0.97 (1.17), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 139 
   PHE   0.015   0.004   PHE A  67 
   TYR   0.055   0.009   TYR A 111 
   ARG   0.038   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 139 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.046   0.011   TYR A 111 
   ARG   0.003   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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

  Ramachandran outliers =   0.73 %
                favored =  93.43 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   3.16
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.54
  MolProbity score      =   1.54

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.024 (Z=  1.686)
  Mean delta:    0.004 (Z=  0.244)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.513 (Z=  1.412)
  Mean delta:    0.825 (Z=  0.399)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   86.851
  Mean delta:   10.866

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.132
  Mean delta:    0.039

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.024
  Mean delta:    0.004

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.024   2241  Z= 0.174
    Angle     :  1.128   5.216   4077  Z= 0.416
    Chirality :  0.039   0.132    176
    Planarity :  0.003   0.024    326
    Dihedral  : 10.207  86.851    768
    Min Nonbonded Distance : 1.012
  
  Molprobity Statistics.
    All-atom Clashscore : 6.77
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.94 (0.71), residues: 137
    helix:  1.38 (0.54), residues: 90
    sheet: -0.35 (1.62), residues: 10
    loop :  1.94 (1.06), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A  43 
   PHE   0.003   0.001   PHE A  15 
   TYR   0.016   0.002   TYR A 111 
   ARG   0.014   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A  43 
   PHE   0.001   0.001   PHE A  15 
   TYR   0.015   0.002   TYR A 111 
   ARG   0.001   0.000   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.037 (Z=  2.916)
  Mean delta:    0.012 (Z=  0.632)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        121.70   132.25   -10.55  1.80e+00  3.43e+01   5.9*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:    0.001 (Z=  0.000)
  Max. delta:   10.546 (Z=  5.859)
  Mean delta:    1.634 (Z=  0.893)

                      ----------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   150.24    29.76  5.00e+00  3.54e+01   6.0*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N
   A 117  PRO  CA        180.00   150.75    29.25  5.00e+00  3.42e+01   5.9*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   152.92    27.08  5.00e+00  2.93e+01   5.4*sigma

  Min. delta:    0.009
  Max. delta:   85.477
  Mean delta:   12.414

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.218
  Mean delta:    0.080

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.048
  Mean delta:    0.011

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2241  Z= 0.450
    Angle     :  1.567  10.546   4077  Z= 0.680
    Chirality :  0.080   0.218    176
    Planarity :  0.008   0.036    326
    Dihedral  : 11.508  85.477    768
    Min Nonbonded Distance : 1.379
  
  Molprobity Statistics.
    All-atom Clashscore : 6.77
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  5.11 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  1.61 %
      Favored  : 96.77 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.00 (0.71), residues: 137
    helix:  0.04 (0.49), residues: 90
    sheet: -1.16 (1.63), residues: 10
    loop :  0.79 (1.24), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.024   0.006   PHE A  67 
   TYR   0.081   0.011   TYR A  50 
   ARG   0.039   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.014   0.005   PHE A  67 
   TYR   0.065   0.014   TYR A  50 
   ARG   0.005   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.77
  RMS(bonds)            =   0.0031
  RMS(angles)           =   1.13
  MolProbity score      =   1.37

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  93.43 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   6.77
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.57
  MolProbity score      =   1.96

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  1.487)
  Mean delta:    0.004 (Z=  0.243)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    4.410 (Z=  1.521)
  Mean delta:    0.818 (Z=  0.395)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.013
  Max. delta:   86.620
  Mean delta:   10.521

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.128
  Mean delta:    0.038

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.025
  Mean delta:    0.004

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.022   2241  Z= 0.173
    Angle     :  1.129   5.379   4077  Z= 0.415
    Chirality :  0.038   0.128    176
    Planarity :  0.003   0.025    326
    Dihedral  :  9.763  86.620    768
    Min Nonbonded Distance : 1.599
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.59 (0.69), residues: 137
    helix:  1.34 (0.53), residues: 86
    sheet: -0.64 (1.69), residues: 10
    loop :  1.21 (0.95), residues: 41
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.003   0.001   PHE A  15 
   TYR   0.014   0.002   TYR A 111 
   ARG   0.014   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.001   0.001   PHE A  15 
   TYR   0.013   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A 127 

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

   A 135  HIS

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.042 (Z=  3.266)
  Mean delta:    0.012 (Z=  0.647)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   130.02    -8.32  1.80e+00  2.14e+01   4.6*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.15     4.45  1.00e+00  1.98e+01   4.4*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.319 (Z=  4.622)
  Mean delta:    1.643 (Z=  0.901)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -151.91   -28.09  5.00e+00  3.16e+01   5.6*sigma

  Min. delta:    0.035
  Max. delta:   84.149
  Mean delta:   11.998

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.207
  Mean delta:    0.078

                       ----------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            0.052       0.093       53.82   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.052
  Mean delta:    0.012

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.042   2241  Z= 0.461
    Angle     :  1.571   8.319   4077  Z= 0.684
    Chirality :  0.078   0.207    176
    Planarity :  0.009   0.052    326
    Dihedral  : 10.975  84.149    768
    Min Nonbonded Distance : 1.514
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.00 %
      Favored  : 98.39 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.22 (0.70), residues: 137
    helix: -0.21 (0.47), residues: 89
    sheet: -1.39 (1.74), residues: 10
    loop :  2.13 (1.17), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.016   0.005   PHE A  67 
   TYR   0.114   0.015   TYR A  81 
   ARG   0.034   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.015   0.005   PHE A  67 
   TYR   0.093   0.018   TYR A  81 
   ARG   0.002   0.000   ARG A 127 

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

   A  66  GLN

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


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

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.13
  MolProbity score      =   1.35

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.57
  MolProbity score      =   1.75

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

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


End of input processing

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

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

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


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

  atoms                 ideal   model   delta   sigma   slack  residual   deviation
   A 127  ARG  NE
   A 127  ARG  CZ          1.33     1.37    -0.04  1.10e-02  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.052 (Z=  4.010)
  Mean delta:    0.018 (Z=  0.992)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   106.56     7.24  1.00e+00  5.25e+01   7.2*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   134.38   -12.68  1.80e+00  4.97e+01   7.0*sigma
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   103.50    10.40  1.80e+00  3.34e+01   5.8*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   106.92     5.68  1.00e+00  3.23e+01   5.7*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   131.85   -10.15  1.80e+00  3.18e+01   5.6*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   131.17    -9.47  1.80e+00  2.77e+01   5.3*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   100.41     9.69  1.90e+00  2.60e+01   5.1*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   107.57     5.03  1.00e+00  2.53e+01   5.0*sigma
   A   7  ASP  CA
   A   7  ASP  CB
   A   7  ASP  CG        112.60   107.62     4.98  1.00e+00  2.48e+01   5.0*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   109.52     7.38  1.50e+00  2.42e+01   4.9*sigma
   A   3  LEU  C
   A   4  ILE  N
   A   4  ILE  CA        121.70   130.26    -8.56  1.80e+00  2.26e+01   4.8*sigma
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        121.70   130.04    -8.34  1.80e+00  2.15e+01   4.6*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.49     4.51  1.00e+00  2.03e+01   4.5*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.53     4.47  1.00e+00  2.00e+01   4.5*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.56     4.44  1.00e+00  1.97e+01   4.4*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.59     4.41  1.00e+00  1.94e+01   4.4*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.60     4.40  1.00e+00  1.94e+01   4.4*sigma
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        121.70   129.62    -7.92  1.80e+00  1.94e+01   4.4*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.65     4.35  1.00e+00  1.90e+01   4.4*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.67     4.33  1.00e+00  1.88e+01   4.3*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   108.60     4.00  1.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   12.684 (Z=  7.244)
  Mean delta:    2.239 (Z=  1.288)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.013
  Max. delta:   82.508
  Mean delta:   12.776

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.480
  Mean delta:    0.112

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.052   2241  Z= 0.706
    Angle     :  2.013  12.684   4077  Z= 0.931
    Chirality :  0.112   0.480    176
    Planarity :  0.012   0.085    326
    Dihedral  : 11.010  82.508    768
    Min Nonbonded Distance : 1.193
  
  Molprobity Statistics.
    All-atom Clashscore : 82.09
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  : 10.95 %
      Favored  : 89.05 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  6.45 %
      Favored  : 89.52 %
    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: -2.14 (0.59), residues: 137
    helix: -0.03 (0.56), residues: 60
    sheet:  None (None), residues: 0
    loop : -2.72 (0.57), residues: 77
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.000   0.000   HIS A 138 
   PHE   0.008   0.002   PHE A  15 
   TYR   0.023   0.003   TYR A  50 
   ARG   0.021   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.000   0.000   HIS A 138 
   PHE   0.007   0.002   PHE A  15 
   TYR   0.017   0.003   TYR A  50 
   ARG   0.004   0.001   ARG A 129 

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

   A 139  HIS
   A  28  GLN
   A  72  ASN
   A 134  HIS

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  3.353)
  Mean delta:    0.012 (Z=  0.640)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.288 (Z=  4.233)
  Mean delta:    1.576 (Z=  0.864)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.019
  Max. delta:   84.676
  Mean delta:   12.412

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.212
  Mean delta:    0.079

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.042
  Mean delta:    0.010

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2241  Z= 0.455
    Angle     :  1.534   7.288   4077  Z= 0.662
    Chirality :  0.079   0.212    176
    Planarity :  0.008   0.038    326
    Dihedral  : 11.565  84.676    768
    Min Nonbonded Distance : 1.687
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.19 %
      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:  0.33 (0.71), residues: 137
    helix: -0.17 (0.50), residues: 86
    sheet: -1.25 (1.72), residues: 10
    loop :  2.09 (1.08), residues: 41
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.017   0.004   PHE A  45 
   TYR   0.056   0.010   TYR A  50 
   ARG   0.034   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.012   0.004   PHE A  67 
   TYR   0.046   0.012   TYR A  50 
   ARG   0.003   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  89.05 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =  82.09
  RMS(bonds)            =   0.0130
  RMS(angles)           =   2.01
  MolProbity score      =   3.42

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  96.35 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   2.71
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.53
  MolProbity score      =   1.46

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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

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

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

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: 0.89 seconds

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.037 (Z=  2.789)
  Mean delta:    0.012 (Z=  0.630)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.053 (Z=  3.861)
  Mean delta:    1.567 (Z=  0.862)

                      ----------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   153.48    26.52  5.00e+00  2.81e+01   5.3*sigma

  Min. delta:    0.025
  Max. delta:   85.508
  Mean delta:   12.106

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.199
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2241  Z= 0.449
    Angle     :  1.527   6.053   4077  Z= 0.661
    Chirality :  0.076   0.199    176
    Planarity :  0.007   0.038    326
    Dihedral  : 11.162  85.508    768
    Min Nonbonded Distance : 1.597
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      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:  0.44 (0.68), residues: 137
    helix: -0.06 (0.47), residues: 92
    sheet: -0.83 (1.60), residues: 10
    loop :  2.36 (1.17), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.017   0.005   PHE A  67 
   TYR   0.055   0.009   TYR A  12 
   ARG   0.040   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.017   0.005   PHE A  67 
   TYR   0.046   0.011   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 119
        1.23 -     1.43: 352
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.353 -0.032 1.00e-02 1.00e+04 1.03e+01
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.20e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.28e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.27e+00
  bond model="   0" pdb=" C   MET A   1 "
       model="   0" pdb=" N   LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.364 -0.035 1.40e-02 5.10e+03 6.13e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.69 -   106.32: 122
      106.32 -   111.95: 2485
      111.95 -   117.58: 465
      117.58 -   123.20: 806
      123.20 -   128.83: 199
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.37    4.23 1.00e+00 1.00e+00 1.79e+01
  angle model="   0" pdb=" C   LYS A  79 "
        model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta    sigma   weight residual
     121.70  127.95   -6.25 1.80e+00 3.09e-01 1.21e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.04   -3.44 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  127.00    4.20 1.30e+00 5.92e-01 1.05e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.83   -4.43 1.40e+00 5.10e-01 1.00e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 972
       17.07 -    34.13: 44
       34.13 -    51.20: 11
       51.20 -    68.26: 3
       68.26 -    85.33: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.70   44.30     0      5.00e+00 4.00e-02 7.85e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.41   34.59     0      5.00e+00 4.00e-02 4.79e+01
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.26   20.74     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.041: 74
       0.041 -    0.082: 48
       0.082 -    0.123: 29
       0.123 -    0.163: 24
       0.163 -    0.204: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality model="   0" pdb=" CG  LEU A  61 "
            model="   0" pdb=" CB  LEU A  61 "
            model="   0" pdb=" CD1 LEU A  61 "
            model="   0" pdb=" CD2 LEU A  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.98e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.067 2.00e-02 2.50e+03   3.10e-02 2.88e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.022 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.061 2.00e-02 2.50e+03   2.42e-02 1.76e+01
        model="   0" pdb=" CG  TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.016 2.00e-02 2.50e+03   3.28e-02 1.08e+01
        model="   0" pdb=" CG  ASP A  36 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.31 -     1.97: 26
        1.97 -     2.62: 2565
        2.62 -     3.28: 6723
        3.28 -     3.94: 7805
        3.94 -     4.60: 11911
  Nonbonded interactions: 29030
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.307 2.440
  nonbonded model="   0" pdb="HD23 LEU A 119 "
            model="   0" pdb="HD12 ILE A 122 "
     model   vdw
     1.483 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.575 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.648 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.660 1.850
  ... (remaining 29025 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.53
  MolProbity score      =   1.51

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

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.031 (Z=  2.184)
  Mean delta:    0.006 (Z=  0.369)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.272 (Z=  1.473)
  Mean delta:    0.830 (Z=  0.395)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   89.489
  Mean delta:   10.838

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.128
  Mean delta:    0.040

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.004

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.004   0.031   2241  Z= 0.263
    Angle     :  1.131   5.229   4077  Z= 0.415
    Chirality :  0.040   0.128    176
    Planarity :  0.003   0.026    326
    Dihedral  : 10.072  89.489    768
    Min Nonbonded Distance : 1.354
  
  Molprobity Statistics.
    All-atom Clashscore : 6.77
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.71 (0.70), residues: 137
    helix:  1.10 (0.52), residues: 90
    sheet: -0.10 (1.70), residues: 10
    loop :  2.06 (1.07), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.004   0.001   PHE A  15 
   TYR   0.014   0.002   TYR A 111 
   ARG   0.011   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.013   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A 129 

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

   A  66  GLN

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.053 (Z=  3.916)
  Mean delta:    0.019 (Z=  1.001)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   100.71    13.19  1.80e+00  5.37e+01   7.3*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   134.09   -12.39  1.80e+00  4.74e+01   6.9*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   105.87     6.73  1.00e+00  4.53e+01   6.7*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   106.19     6.41  1.00e+00  4.11e+01   6.4*sigma
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   107.75     6.05  1.00e+00  3.66e+01   6.0*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   131.84   -10.14  1.80e+00  3.17e+01   5.6*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   108.46     8.44  1.50e+00  3.17e+01   5.6*sigma
   A  15  PHE  CA
   A  15  PHE  CB
   A  15  PHE  CG        113.80   108.27     5.53  1.00e+00  3.06e+01   5.5*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   107.39     5.21  1.00e+00  2.71e+01   5.2*sigma
   A  70  LEU  C
   A  70  LEU  CA
   A  70  LEU  CB        110.10   100.39     9.71  1.90e+00  2.61e+01   5.1*sigma
   A 110  ASP  CA
   A 110  ASP  CB
   A 110  ASP  CG        112.60   107.56     5.04  1.00e+00  2.54e+01   5.0*sigma
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        121.70   130.64    -8.94  1.80e+00  2.47e+01   5.0*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   130.59    -8.89  1.80e+00  2.44e+01   4.9*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   107.69     4.91  1.00e+00  2.41e+01   4.9*sigma
   A  97  SER  N
   A  97  SER  CA
   A  97  SER  CB        110.50   118.65    -8.15  1.70e+00  2.30e+01   4.8*sigma
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        121.70   130.02    -8.32  1.80e+00  2.14e+01   4.6*sigma
   A 138  HIS  CA
   A 138  HIS  CB
   A 138  HIS  CG        113.80   118.41    -4.61  1.00e+00  2.12e+01   4.6*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.49     4.51  1.00e+00  2.03e+01   4.5*sigma
   A   7  ASP  CA
   A   7  ASP  CB
   A   7  ASP  CG        112.60   108.10     4.50  1.00e+00  2.02e+01   4.5*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.51     4.49  1.00e+00  2.02e+01   4.5*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.52     4.48  1.00e+00  2.01e+01   4.5*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.54     4.46  1.00e+00  1.99e+01   4.5*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   108.15     4.45  1.00e+00  1.98e+01   4.4*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.56     4.44  1.00e+00  1.97e+01   4.4*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   108.17     4.43  1.00e+00  1.96e+01   4.4*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.61     4.39  1.00e+00  1.92e+01   4.4*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.63     4.37  1.00e+00  1.91e+01   4.4*sigma
   A  28  GLN  CB
   A  28  GLN  CG
   A  28  GLN  CD        112.60   105.20     7.40  1.70e+00  1.89e+01   4.4*sigma
   A 107  LEU  C
   A 108  ILE  N
   A 108  ILE  CA        121.70   129.36    -7.66  1.80e+00  1.81e+01   4.3*sigma
   A 136  HIS  CA
   A 136  HIS  CB
   A 136  HIS  CG        113.80   109.59     4.21  1.00e+00  1.78e+01   4.2*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   129.23    -7.53  1.80e+00  1.75e+01   4.2*sigma
   A  10  LYS  C
   A  10  LYS  CA
   A  10  LYS  CB        110.10   102.21     7.89  1.90e+00  1.72e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   13.186 (Z=  7.326)
  Mean delta:    2.353 (Z=  1.368)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   85.111
  Mean delta:   14.161

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.483
  Mean delta:    0.128

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.121
  Mean delta:    0.019

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.053   2241  Z= 0.713
    Angle     :  2.084  13.186   4077  Z= 0.978
    Chirality :  0.128   0.483    176
    Planarity :  0.014   0.121    326
    Dihedral  : 11.992  85.111    768
    Min Nonbonded Distance : 1.191
  
  Molprobity Statistics.
    All-atom Clashscore : 72.62
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  9.49 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  8.87 %
      Favored  : 87.90 %
    Cbeta Deviations :  1.52 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.48 (0.61), residues: 137
    helix:  0.26 (0.56), residues: 68
    sheet:  None (None), residues: 0
    loop : -3.89 (0.53), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.010   0.003   PHE A  67 
   TYR   0.019   0.004   TYR A 105 
   ARG   0.037   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.009   0.002   PHE A  67 
   TYR   0.013   0.003   TYR A 105 
   ARG   0.010   0.003   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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


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

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.77
  RMS(bonds)            =   0.0041
  RMS(angles)           =   1.13
  MolProbity score      =   1.37

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

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

  Ramachandran outliers =   2.19 %
                favored =  88.32 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     2
  Clashscore            =  72.62
  RMS(bonds)            =   0.0132
  RMS(angles)           =   2.08
  MolProbity score      =   3.31

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.033 (Z=  2.343)
  Mean delta:    0.006 (Z=  0.359)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.083 (Z=  1.516)
  Mean delta:    0.775 (Z=  0.368)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   78.616
  Mean delta:   11.748

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.134
  Mean delta:    0.040

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.004

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.004   0.033   2241  Z= 0.256
    Angle     :  1.118   5.274   4077  Z= 0.406
    Chirality :  0.040   0.134    176
    Planarity :  0.003   0.026    326
    Dihedral  : 10.552  78.616    768
    Min Nonbonded Distance : 1.503
  
  Molprobity Statistics.
    All-atom Clashscore : 7.67
    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:  1.89 (0.69), residues: 137
    helix:  1.53 (0.51), residues: 92
    sheet: -1.46 (1.62), residues: 10
    loop :  1.73 (1.07), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 137 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.017   0.002   TYR A 111 
   ARG   0.012   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 137 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.016   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A  58 

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

   A  66  GLN

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

  Time building chain proxies: 1.05, per 1000 atoms: 0.47
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (52.444, 42.893, 61.049, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.00 %
                favored =  99.27 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.67
  RMS(bonds)            =   0.0041
  RMS(angles)           =   1.12
  MolProbity score      =   1.42

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.047 (Z=  3.732)
  Mean delta:    0.018 (Z=  0.997)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   102.43    11.47  1.80e+00  4.06e+01   6.4*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   133.04   -11.34  1.80e+00  3.97e+01   6.3*sigma
   A   7  ASP  CA
   A   7  ASP  CB
   A   7  ASP  CG        112.60   106.31     6.29  1.00e+00  3.95e+01   6.3*sigma
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   107.52     6.28  1.00e+00  3.95e+01   6.3*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   132.58   -10.88  1.80e+00  3.65e+01   6.0*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   106.61     5.99  1.00e+00  3.59e+01   6.0*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   108.45     8.45  1.50e+00  3.17e+01   5.6*sigma
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        121.70   111.77     9.93  1.80e+00  3.04e+01   5.5*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   107.14     5.46  1.00e+00  2.98e+01   5.5*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   107.36     5.24  1.00e+00  2.74e+01   5.2*sigma
   A  70  LEU  C
   A  71  ILE  N
   A  71  ILE  CA        121.70   131.12    -9.42  1.80e+00  2.74e+01   5.2*sigma
   A   3  LEU  C
   A   4  ILE  N
   A   4  ILE  CA        121.70   130.99    -9.29  1.80e+00  2.66e+01   5.2*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   107.75     4.85  1.00e+00  2.36e+01   4.9*sigma
   A  91  TYR  CA
   A  91  TYR  CB
   A  91  TYR  CG        113.90   105.23     8.67  1.80e+00  2.32e+01   4.8*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   107.80     4.80  1.00e+00  2.31e+01   4.8*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   130.26    -8.56  1.80e+00  2.26e+01   4.8*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   105.44     8.46  1.80e+00  2.21e+01   4.7*sigma
   A   2  LEU  C
   A   2  LEU  CA
   A   2  LEU  CB        110.10   101.52     8.58  1.90e+00  2.04e+01   4.5*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.51     4.49  1.00e+00  2.02e+01   4.5*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.52     4.48  1.00e+00  2.01e+01   4.5*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.55     4.45  1.00e+00  1.98e+01   4.5*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.55     4.45  1.00e+00  1.98e+01   4.4*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.57     4.43  1.00e+00  1.96e+01   4.4*sigma
   A  71  ILE  C
   A  72  ASN  N
   A  72  ASN  CA        121.70   113.74     7.96  1.80e+00  1.95e+01   4.4*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.61     4.39  1.00e+00  1.93e+01   4.4*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.65     4.35  1.00e+00  1.89e+01   4.3*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   108.33     4.27  1.00e+00  1.82e+01   4.3*sigma
   A   8  GLU  CB
   A   8  GLU  CG
   A   8  GLU  CD        112.60   105.40     7.20  1.70e+00  1.79e+01   4.2*sigma
   A 110  ASP  CA
   A 110  ASP  CB
   A 110  ASP  CG        112.60   108.48     4.12  1.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   11.468 (Z=  6.371)
  Mean delta:    2.252 (Z=  1.311)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.033
  Max. delta:   85.178
  Mean delta:   13.217

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.489
  Mean delta:    0.116

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.114
  Mean delta:    0.016

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.047   2241  Z= 0.709
    Angle     :  2.009  11.468   4077  Z= 0.941
    Chirality :  0.116   0.489    176
    Planarity :  0.012   0.114    326
    Dihedral  : 11.154  85.178    768
    Min Nonbonded Distance : 1.206
  
  Molprobity Statistics.
    All-atom Clashscore : 85.25
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  : 10.22 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  7.26 %
      Favored  : 88.71 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.18 (0.60), residues: 137
    helix: -0.21 (0.53), residues: 69
    sheet:  None (None), residues: 0
    loop : -2.89 (0.60), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.024   0.003   TYR A  50 
   ARG   0.020   0.005   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.010   0.002   PHE A  67 
   TYR   0.018   0.002   TYR A  50 
   ARG   0.005   0.002   ARG A 127 

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

   A 139  HIS
   A  72  ASN

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


  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.028 (Z=  1.324)
  Mean delta:    0.004 (Z=  0.239)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.970 (Z=  1.638)
  Mean delta:    0.812 (Z=  0.389)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.015
  Max. delta:   84.575
  Mean delta:   11.345

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.137
  Mean delta:    0.039

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.004

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.028   2241  Z= 0.170
    Angle     :  1.122   5.354   4077  Z= 0.411
    Chirality :  0.039   0.137    176
    Planarity :  0.003   0.026    326
    Dihedral  : 10.547  84.575    768
    Min Nonbonded Distance : 1.409
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  2.37 (0.70), residues: 137
    helix:  1.61 (0.51), residues: 91
    sheet: -0.18 (1.76), residues: 10
    loop :  2.42 (1.10), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.018   0.002   TYR A 111 
   ARG   0.013   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.001   0.001   PHE A  45 
   TYR   0.016   0.002   TYR A 111 
   ARG   0.001   0.000   ARG A 127 

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

   A 134  HIS
   A 138  HIS

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

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (57.253, 59.635, 57.517, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   1.46 %
                favored =  88.32 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     1
  Clashscore            =  85.25
  RMS(bonds)            =   0.0132
  RMS(angles)           =   2.01
  MolProbity score      =   3.45

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  3.115)
  Mean delta:    0.012 (Z=  0.638)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   116.82    -4.22  1.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.630 (Z=  4.220)
  Mean delta:    1.612 (Z=  0.882)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   148.06    31.94  5.00e+00  4.08e+01   6.4*sigma

  Min. delta:    0.008
  Max. delta:   88.434
  Mean delta:   12.478

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.235
  Mean delta:    0.079

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2241  Z= 0.454
    Angle     :  1.554   6.630   4077  Z= 0.673
    Chirality :  0.079   0.235    176
    Planarity :  0.008   0.053    326
    Dihedral  : 11.233  88.434    768
    Min Nonbonded Distance : 1.649
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.92 %
      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 : 0.76 %
  
  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:  0.20 (0.70), residues: 137
    helix: -0.13 (0.50), residues: 88
    sheet: -0.85 (1.71), residues: 10
    loop :  1.64 (1.13), residues: 39
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 139 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.057   0.010   TYR A  12 
   ARG   0.037   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 139 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.048   0.011   TYR A  12 
   ARG   0.003   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   4.51
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.12
  MolProbity score      =   1.23

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.025 (Z=  1.793)
  Mean delta:    0.005 (Z=  0.307)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.233 (Z=  1.535)
  Mean delta:    0.842 (Z=  0.404)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.004
  Max. delta:   84.614
  Mean delta:   11.931

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.117
  Mean delta:    0.041

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.004

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.004   0.025   2241  Z= 0.219
    Angle     :  1.143   5.381   4077  Z= 0.421
    Chirality :  0.041   0.117    176
    Planarity :  0.003   0.026    326
    Dihedral  : 11.094  84.614    768
    Min Nonbonded Distance : 0.972
  
  Molprobity Statistics.
    All-atom Clashscore : 19.85
    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     : 28.57 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.12 (0.67), residues: 137
    helix:  1.02 (0.51), residues: 86
    sheet: -2.76 (1.25), residues: 10
    loop :  1.49 (0.94), residues: 41
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.016   0.003   TYR A 105 
   ARG   0.012   0.003   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.015   0.003   TYR A 111 
   ARG   0.005   0.001   ARG A 129 

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

   A 135  HIS

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


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

  Ramachandran outliers =   0.73 %
                favored =  96.35 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   4.51
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.55
  MolProbity score      =   1.47

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.028 (Z=  1.461)
  Mean delta:    0.004 (Z=  0.243)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.123 (Z=  1.461)
  Mean delta:    0.811 (Z=  0.389)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   87.640
  Mean delta:   11.226

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.132
  Mean delta:    0.043

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.028   2241  Z= 0.174
    Angle     :  1.136   5.305   4077  Z= 0.416
    Chirality :  0.043   0.132    176
    Planarity :  0.003   0.025    326
    Dihedral  :  9.744  87.640    768
    Min Nonbonded Distance : 0.996
  
  Molprobity Statistics.
    All-atom Clashscore : 13.53
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.81 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.74 (0.68), residues: 137
    helix:  1.02 (0.50), residues: 89
    sheet: -1.04 (1.46), residues: 10
    loop :  2.65 (1.02), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.016   0.002   TYR A 111 
   ARG   0.012   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.015   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A 129 

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

   A 134  HIS
   A 135  HIS

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

  Ramachandran outliers =   0.00 %
                favored =  99.27 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  19.85
  RMS(bonds)            =   0.0036
  RMS(angles)           =   1.14
  MolProbity score      =   1.79

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  13.53
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.14
  MolProbity score      =   1.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.021 (Z=  1.274)
  Mean delta:    0.004 (Z=  0.248)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    5.505 (Z=  1.845)
  Mean delta:    0.849 (Z=  0.401)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.015
  Max. delta:   88.882
  Mean delta:   11.074

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.134
  Mean delta:    0.040

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.024
  Mean delta:    0.003

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.021   2241  Z= 0.177
    Angle     :  1.141   5.505   4077  Z= 0.419
    Chirality :  0.040   0.134    176
    Planarity :  0.003   0.024    326
    Dihedral  : 10.356  88.882    768
    Min Nonbonded Distance : 1.371
  
  Molprobity Statistics.
    All-atom Clashscore : 13.08
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.81 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.22 (0.68), residues: 137
    helix:  0.71 (0.53), residues: 85
    sheet: -0.97 (1.60), residues: 10
    loop :  1.96 (0.95), residues: 42
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.003   0.001   PHE A  15 
   TYR   0.015   0.002   TYR A 111 
   ARG   0.012   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.001   0.001   PHE A  67 
   TYR   0.014   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A  58 

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

   A 135  HIS

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


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

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  13.08
  RMS(bonds)            =   0.0031
  RMS(angles)           =   1.14
  MolProbity score      =   1.63

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (47.859, 44.857, 77.292, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

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

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

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (46.903, 47.372, 74.809, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      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: 1.19, per 1000 atoms: 0.54
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.542, 58.707, 62.969, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

  Time building chain proxies: 1.19, per 1000 atoms: 0.54
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (71.38, 69.761, 52.584, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

  Time building chain proxies: 1.24, per 1000 atoms: 0.56
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (46.973, 65.776, 69.866, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.042 (Z=  2.707)
  Mean delta:    0.012 (Z=  0.598)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.199 (Z=  3.539)
  Mean delta:    1.565 (Z=  0.860)

                      ----------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   144.39    35.61  5.00e+00  5.07e+01   7.1*sigma

  Min. delta:    0.021
  Max. delta:   88.625
  Mean delta:   12.544

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.192
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.041
  Mean delta:    0.010

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.042   2241  Z= 0.425
    Angle     :  1.526   6.199   4077  Z= 0.660
    Chirality :  0.076   0.192    176
    Planarity :  0.007   0.031    326
    Dihedral  : 11.150  88.625    768
    Min Nonbonded Distance : 1.598
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  0.81 %
      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: -0.24 (0.70), residues: 137
    helix: -0.39 (0.48), residues: 90
    sheet: -0.86 (1.68), residues: 10
    loop :  1.29 (1.22), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS A 139 
   PHE   0.020   0.004   PHE A  45 
   TYR   0.058   0.010   TYR A 111 
   ARG   0.034   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS A 139 
   PHE   0.012   0.005   PHE A  45 
   TYR   0.049   0.012   TYR A 111 
   ARG   0.004   0.001   ARG A  58 

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

  No backwards Asn/Gln/His sidechains found.

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


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

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

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

  Ramachandran outliers =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.53
  MolProbity score      =   1.75

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: 0.99
  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.

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: 86
        1.23 -     1.43: 385
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.67e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 8.85e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.79e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.62e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.56e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.71 -   106.41: 115
      106.41 -   112.12: 2541
      112.12 -   117.83: 422
      117.83 -   123.54: 860
      123.54 -   129.24: 139
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.54    4.06 1.00e+00 1.00e+00 1.65e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.26    4.94 1.30e+00 5.92e-01 1.44e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.96    3.64 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.24   -4.84 1.40e+00 5.10e-01 1.20e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.93   -3.33 1.00e+00 1.00e+00 1.11e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 969
       17.06 -    34.11: 45
       34.11 -    51.17: 14
       51.17 -    68.22: 2
       68.22 -    85.27: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.10   20.90     0      5.00e+00 4.00e-02 1.75e+01
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.53   15.47     0      5.00e+00 4.00e-02 9.57e+00
  dihedral model="   0" pdb=" CA  LYS A 113 "
           model="   0" pdb=" C   LYS A 113 "
           model="   0" pdb=" N   PRO A 114 "
           model="   0" pdb=" CA  PRO A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.72   15.28     0      5.00e+00 4.00e-02 9.34e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 73
       0.039 -    0.078: 49
       0.078 -    0.117: 30
       0.117 -    0.156: 18
       0.156 -    0.194: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.46e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.98e-01
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.50e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.064 2.00e-02 2.50e+03   2.75e-02 2.27e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.056 2.00e-02 2.50e+03   2.24e-02 1.50e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.056 2.00e-02 2.50e+03   2.17e-02 1.41e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 309
        2.28 -     2.86: 5128
        2.86 -     3.44: 5435
        3.44 -     4.02: 7236
        4.02 -     4.60: 10722
  Nonbonded interactions: 28830
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.704 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.747 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.774 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.782 1.850
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.823 1.850
  ... (remaining 28825 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  3.111)
  Mean delta:    0.012 (Z=  0.631)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   129.61    -7.91  1.80e+00  1.93e+01   4.4*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.908 (Z=  4.393)
  Mean delta:    1.606 (Z=  0.885)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -157.89   -22.11  5.00e+00  1.96e+01   4.4*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   160.00    20.00  5.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.031
  Max. delta:   85.025
  Mean delta:   12.857

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.199
  Mean delta:    0.078

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.074
  Mean delta:    0.011

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2241  Z= 0.450
    Angle     :  1.552   7.908   4077  Z= 0.675
    Chirality :  0.078   0.199    176
    Planarity :  0.008   0.056    326
    Dihedral  : 11.467  85.025    768
    Min Nonbonded Distance : 1.587
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  3.23 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.22 (0.68), residues: 137
    helix: -0.08 (0.49), residues: 85
    sheet: -1.31 (1.64), residues: 10
    loop :  0.45 (1.06), residues: 42
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.018   0.004   PHE A  45 
   TYR   0.067   0.010   TYR A 111 
   ARG   0.061   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.056   0.013   TYR A 111 
   ARG   0.006   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.17 seconds

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

  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   3.16
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.55
  MolProbity score      =   1.75

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 113
        1.23 -     1.43: 358
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.356 -0.035 1.00e-02 1.00e+04 1.24e+01
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.13e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.90e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.60e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.85e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.18 -   105.99: 83
      105.99 -   111.80: 2494
      111.80 -   117.61: 492
      117.61 -   123.42: 852
      123.42 -   129.22: 156
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.39    4.21 1.00e+00 1.00e+00 1.77e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.82    3.78 1.00e+00 1.00e+00 1.43e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.22   -4.82 1.40e+00 5.10e-01 1.19e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.99   -3.39 1.00e+00 1.00e+00 1.15e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  115.89   -3.29 1.00e+00 1.00e+00 1.08e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.77: 968
       16.77 -    33.54: 46
       33.54 -    50.31: 12
       50.31 -    67.09: 4
       67.09 -    83.86: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.79   32.21     0      5.00e+00 4.00e-02 4.15e+01
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.41   19.59     0      5.00e+00 4.00e-02 1.53e+01
  dihedral model="   0" pdb=" CA  LYS A 113 "
           model="   0" pdb=" C   LYS A 113 "
           model="   0" pdb=" N   PRO A 114 "
           model="   0" pdb=" CA  PRO A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.71   18.29     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 74
       0.047 -    0.094: 58
       0.094 -    0.142: 29
       0.142 -    0.189: 13
       0.189 -    0.236: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality model="   0" pdb=" CG  LEU A 119 "
            model="   0" pdb=" CB  LEU A 119 "
            model="   0" pdb=" CD1 LEU A 119 "
            model="   0" pdb=" CD2 LEU A 119 "
    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: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.060 2.00e-02 2.50e+03   2.57e-02 1.97e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.049 2.00e-02 2.50e+03   1.90e-02 1.08e+01
        model="   0" pdb=" CG  TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.014 2.00e-02 2.50e+03   2.77e-02 7.68e+00
        model="   0" pdb=" CG  ASP A  36 "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 173
        2.21 -     2.81: 4455
        2.81 -     3.40: 5976
        3.40 -     4.00: 7357
        4.00 -     4.60: 11082
  Nonbonded interactions: 29043
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.611 1.850
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HG  SER A  90 "
     model   vdw
     1.615 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.617 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.638 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.704 1.850
  ... (remaining 29038 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  3.127)
  Mean delta:    0.012 (Z=  0.661)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.922 (Z=  3.750)
  Mean delta:    1.575 (Z=  0.861)

                      ----------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   153.64    26.36  5.00e+00  2.78e+01   5.3*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   155.48    24.52  5.00e+00  2.40e+01   4.9*sigma

  Min. delta:    0.038
  Max. delta:   78.303
  Mean delta:   12.387

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:    0.180
  Mean delta:    0.074

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.042
  Mean delta:    0.010

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2241  Z= 0.470
    Angle     :  1.524   6.922   4077  Z= 0.659
    Chirality :  0.074   0.180    176
    Planarity :  0.008   0.032    326
    Dihedral  : 10.895  78.303    768
    Min Nonbonded Distance : 1.642
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      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: -0.05 (0.70), residues: 137
    helix: -0.07 (0.49), residues: 88
    sheet: -0.72 (1.74), residues: 10
    loop :  0.78 (1.18), residues: 39
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.018   0.005   PHE A  45 
   TYR   0.058   0.010   TYR A 111 
   ARG   0.036   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.012   0.005   PHE A  67 
   TYR   0.049   0.011   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

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

   A  66  GLN

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


  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0088
  RMS(angles)           =   1.52
  MolProbity score      =   1.72

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.12, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (48.992, 78.429, 46.139, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  3.002)
  Mean delta:    0.012 (Z=  0.632)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.261 (Z=  3.816)
  Mean delta:    1.591 (Z=  0.878)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.039
  Max. delta:   84.775
  Mean delta:   11.886

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.188
  Mean delta:    0.074

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.059
  Mean delta:    0.012

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.041   2241  Z= 0.450
    Angle     :  1.533   6.261   4077  Z= 0.668
    Chirality :  0.074   0.188    176
    Planarity :  0.009   0.046    326
    Dihedral  : 10.502  84.775    768
    Min Nonbonded Distance : 1.688
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  0.73 %
      Favored  : 97.08 %
    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:  0.24 (0.68), residues: 137
    helix: -0.12 (0.48), residues: 92
    sheet: -1.23 (1.70), residues: 10
    loop :  2.09 (1.13), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.018   0.005   PHE A  45 
   TYR   0.073   0.011   TYR A  50 
   ARG   0.049   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.012   0.004   PHE A  67 
   TYR   0.060   0.013   TYR A  50 
   ARG   0.004   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  3.071)
  Mean delta:    0.012 (Z=  0.611)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.231 (Z=  3.911)
  Mean delta:    1.606 (Z=  0.878)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   159.19    20.81  5.00e+00  1.73e+01   4.2*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   159.67    20.33  5.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.004
  Max. delta:   85.543
  Mean delta:   12.974

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.205
  Mean delta:    0.081

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2241  Z= 0.435
    Angle     :  1.557   6.231   4077  Z= 0.672
    Chirality :  0.081   0.205    176
    Planarity :  0.007   0.046    326
    Dihedral  : 11.236  85.543    768
    Min Nonbonded Distance : 1.457
  
  Molprobity Statistics.
    All-atom Clashscore : 6.77
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.84 %
      Favored  : 92.74 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.64 (0.71), residues: 137
    helix: -1.18 (0.52), residues: 79
    sheet:  None (None), residues: 0
    loop :  1.08 (0.90), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 139 
   PHE   0.016   0.004   PHE A  45 
   TYR   0.060   0.009   TYR A 111 
   ARG   0.037   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 139 
   PHE   0.009   0.003   PHE A  45 
   TYR   0.051   0.010   TYR A 111 
   ARG   0.002   0.001   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)----------                  

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

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


  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A 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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   6.77
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.56
  MolProbity score      =   1.83

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.19 %
                favored =  97.08 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   3.16
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.53
  MolProbity score      =   1.27

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

  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.85 seconds

  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: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 114
        1.23 -     1.43: 357
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.22e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.48e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.53e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 7.04e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.70e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       99.91 -   105.85: 72
      105.85 -   111.79: 2511
      111.79 -   117.73: 496
      117.73 -   123.67: 874
      123.67 -   129.60: 124
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.70    3.90 1.00e+00 1.00e+00 1.52e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.60   -5.20 1.40e+00 5.10e-01 1.38e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.08    3.52 1.00e+00 1.00e+00 1.24e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.02   -3.42 1.00e+00 1.00e+00 1.17e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  127.09    4.11 1.30e+00 5.92e-01 1.00e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 974
       17.99 -    35.98: 36
       35.98 -    53.97: 17
       53.97 -    71.96: 3
       71.96 -    89.95: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.78   21.22     0      5.00e+00 4.00e-02 1.80e+01
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.22   17.78     0      5.00e+00 4.00e-02 1.26e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.67   16.33     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 76
       0.042 -    0.083: 45
       0.083 -    0.125: 35
       0.125 -    0.166: 17
       0.166 -    0.208: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality model="   0" pdb=" CG  LEU A  53 "
            model="   0" pdb=" CB  LEU A  53 "
            model="   0" pdb=" CD1 LEU A  53 "
            model="   0" pdb=" CD2 LEU A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.55e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.066 2.00e-02 2.50e+03   2.90e-02 2.52e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.057 2.00e-02 2.50e+03   2.26e-02 1.54e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.051 2.00e-02 2.50e+03   2.00e-02 1.20e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 215
        2.25 -     2.84: 4767
        2.84 -     3.42: 5710
        3.42 -     4.01: 7289
        4.01 -     4.60: 10844
  Nonbonded interactions: 28825
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.661 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.673 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.746 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.760 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.779 1.850
  ... (remaining 28820 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 91
        1.23 -     1.43: 380
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.354 -0.033 1.00e-02 1.00e+04 1.08e+01
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.38e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.386 -0.032 1.10e-02 8.26e+03 8.43e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.32e+00
  bond model="   0" pdb=" CE1 HIS A  43 "
       model="   0" pdb=" NE2 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.19e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.50 -   106.18: 99
      106.18 -   111.86: 2496
      111.86 -   117.54: 472
      117.54 -   123.22: 816
      123.22 -   128.90: 194
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.40    4.80 1.30e+00 5.92e-01 1.36e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.93    3.67 1.00e+00 1.00e+00 1.35e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.93    3.67 1.00e+00 1.00e+00 1.34e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.90   -4.50 1.40e+00 5.10e-01 1.03e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  127.03    4.17 1.30e+00 5.92e-01 1.03e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.17: 960
       16.17 -    32.34: 45
       32.34 -    48.50: 22
       48.50 -    64.67: 4
       64.67 -    80.84: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.23   25.77     0      5.00e+00 4.00e-02 2.66e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.36   18.64     0      5.00e+00 4.00e-02 1.39e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.35   16.65     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.039: 74
       0.039 -    0.078: 42
       0.078 -    0.116: 34
       0.116 -    0.154: 22
       0.154 -    0.193: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.29e-01
  chirality model="   0" pdb=" CG  LEU A 119 "
            model="   0" pdb=" CB  LEU A 119 "
            model="   0" pdb=" CD1 LEU A 119 "
            model="   0" pdb=" CD2 LEU A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.06e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.05e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.062 2.00e-02 2.50e+03   2.71e-02 2.20e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.053 2.00e-02 2.50e+03   2.13e-02 1.36e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.046 2.00e-02 2.50e+03   1.77e-02 9.35e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 176
        2.21 -     2.81: 4388
        2.81 -     3.40: 5948
        3.40 -     4.00: 7232
        4.00 -     4.60: 10935
  Nonbonded interactions: 28679
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.612 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.719 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.720 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.746 1.850
  ... (remaining 28674 not shown)

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.88 seconds

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

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.

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 121
        1.23 -     1.43: 353
        1.43 -     1.62: 657
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.47e+01
  bond model="   0" pdb=" NE  ARG A 127 "
       model="   0" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.41e+01
  bond model="   0" pdb=" NE  ARG A 129 "
       model="   0" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.36e+01
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.32e+01
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.27e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       95.80 -   103.15: 17
      103.15 -   110.50: 2158
      110.50 -   117.85: 967
      117.85 -   125.20: 890
      125.20 -   132.55: 45
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90   99.59   14.31 1.80e+00 3.09e-01 6.32e+01
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  106.45    7.35 1.00e+00 1.00e+00 5.40e+01
  angle model="   0" pdb=" CA  ASP A  88 "
        model="   0" pdb=" CB  ASP A  88 "
        model="   0" pdb=" CG  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     112.60  105.49    7.11 1.00e+00 1.00e+00 5.05e+01
  angle model="   0" pdb=" CA  ASN A  72 "
        model="   0" pdb=" CB  ASN A  72 "
        model="   0" pdb=" CG  ASN A  72 "
      ideal   model   delta    sigma   weight residual
     112.60  105.82    6.78 1.00e+00 1.00e+00 4.59e+01
  angle model="   0" pdb=" CA  ASP A 103 "
        model="   0" pdb=" CB  ASP A 103 "
        model="   0" pdb=" CG  ASP A 103 "
      ideal   model   delta    sigma   weight residual
     112.60  106.54    6.06 1.00e+00 1.00e+00 3.68e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 966
       17.75 -    35.49: 53
       35.49 -    53.23: 3
       53.23 -    70.98: 6
       70.98 -    88.72: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" CB  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.47  -11.13     0      2.50e+00 1.60e-01 1.98e+01
  dihedral model="   0" pdb=" N   ASN A  72 "
           model="   0" pdb=" C   ASN A  72 "
           model="   0" pdb=" CA  ASN A  72 "
           model="   0" pdb=" CB  ASN A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.78  -10.98     0      2.50e+00 1.60e-01 1.93e+01
  dihedral model="   0" pdb=" C   LYS A  19 "
           model="   0" pdb=" N   LYS A  19 "
           model="   0" pdb=" CA  LYS A  19 "
           model="   0" pdb=" CB  LYS A  19 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.50  -10.10     0      2.50e+00 1.60e-01 1.63e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 130
       0.102 -    0.203: 31
       0.203 -    0.305: 8
       0.305 -    0.406: 4
       0.406 -    0.508: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.45e+00
  chirality model="   0" pdb=" CA  ASN A  72 "
            model="   0" pdb=" N   ASN A  72 "
            model="   0" pdb=" C   ASN A  72 "
            model="   0" pdb=" CB  ASN A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.09e+00
  chirality model="   0" pdb=" CA  PRO A 102 "
            model="   0" pdb=" N   PRO A 102 "
            model="   0" pdb=" C   PRO A 102 "
            model="   0" pdb=" CB  PRO A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.31    0.41 2.00e-01 2.50e+01 4.17e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ILE A  51 "    0.073 5.00e-02 4.00e+02   1.11e-01 1.95e+01
        model="   0" pdb=" N   PRO A  52 "   -0.191 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  52 "    0.058 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  52 "    0.061 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "    0.061 5.00e-02 4.00e+02   9.38e-02 1.41e+01
        model="   0" pdb=" N   PRO A  54 "   -0.162 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "    0.051 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "    0.050 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ASP A 116 "   -0.056 5.00e-02 4.00e+02   8.55e-02 1.17e+01
        model="   0" pdb=" N   PRO A 117 "    0.148 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A 117 "   -0.048 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A 117 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 88
        2.00 -     2.65: 3308
        2.65 -     3.30: 6589
        3.30 -     3.95: 7657
        3.95 -     4.60: 11952
  Nonbonded interactions: 29594
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  78 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.353 2.270
  nonbonded model="   0" pdb="HD12 LEU A   2 "
            model="   0" pdb=" H   ILE A   4 "
     model   vdw
     1.404 2.270
  nonbonded model="   0" pdb="HG12 ILE A 131 "
            model="   0" pdb=" HB2 HIS A 134 "
     model   vdw
     1.420 2.440
  nonbonded model="   0" pdb=" HE1 PHE A  67 "
            model="   0" pdb=" HG  LEU A  99 "
     model   vdw
     1.423 2.270
  nonbonded model="   0" pdb=" HB2 LYS A  10 "
            model="   0" pdb=" HD3 LYS A  19 "
     model   vdw
     1.432 2.440
  ... (remaining 29589 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: 6
        1.23 -     1.42: 458
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.294  0.035 1.40e-02 5.10e+03 6.25e+00
  bond model="   0" pdb=" C   ILE A  86 "
       model="   0" pdb=" N   GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.024 1.40e-02 5.10e+03 2.86e+00
  bond model="   0" pdb=" C   HIS A 136 "
       model="   0" pdb=" N   HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.51e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.88e+00
  bond model="   0" pdb=" C   THR A  20 "
       model="   0" pdb=" N   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.58e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.35 -   106.45: 50
      106.45 -   112.54: 2689
      112.54 -   118.64: 448
      118.64 -   124.74: 834
      124.74 -   130.84: 56
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" N   GLY A  87 "
        model="   0" pdb=" CA  GLY A  87 "
        model="   0" pdb=" C   GLY A  87 "
      ideal   model   delta    sigma   weight residual
     113.30  107.85    5.45 2.90e+00 1.19e-01 3.54e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.45   -5.45 3.00e+00 1.11e-01 3.30e+00
  angle model="   0" pdb=" C   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  103.79    5.21 3.00e+00 1.11e-01 3.02e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.99    5.01 3.00e+00 1.11e-01 2.79e+00
  angle model="   0" pdb=" NE  ARG A  58 "
        model="   0" pdb=" CZ  ARG A  58 "
        model="   0" pdb=" NH1 ARG A  58 "
      ideal   model   delta    sigma   weight residual
     121.50  119.84    1.66 1.00e+00 1.00e+00 2.76e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 976
       16.80 -    33.60: 36
       33.60 -    50.39: 11
       50.39 -    67.19: 8
       67.19 -    83.99: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   GLU A 123 "
           model="   0" pdb=" CA  GLU A 123 "
           model="   0" pdb=" CB  GLU A 123 "
           model="   0" pdb=" CG  GLU A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.00   55.00     3      1.50e+01 4.44e-03 9.32e+00
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   64.27  -64.27     1      3.00e+01 1.11e-03 6.04e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -96.01  -83.99     2      3.00e+01 1.11e-03 5.27e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 96
       0.025 -    0.050: 46
       0.050 -    0.075: 21
       0.075 -    0.100: 7
       0        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
.100 -    0.125: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.92e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.10 2.00e-01 2.50e+01 2.74e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.017 5.00e-02 4.00e+02   2.63e-02 1.10e+00
        model="   0" pdb=" N   PRO A   6 "   -0.045 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.015 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.014 2.00e-02 2.50e+03   5.98e-03 1.07e+00
        model="   0" pdb=" CG  TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "    0.009 2.00e-02 2.50e+03   7.50e-03 8.43e-01
        model="   0" pdb=" CD  GLN A  66 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "    0.011 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 169
        2.19 -     2.79: 4594
        2.79 -     3.40: 6001
        3.40 -     4.00: 7715
        4.00 -     4.60: 11931
  Nonbonded interactions: 30410
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 TYR A  89 "
            model="   0" pdb=" HB3 LYS A 101 "
     model   vdw
     1.591 2.440
  nonbonded model="   0" pdb="HH11 ARG A  21 "
            model="   0" pdb=" OD2 ASP A  29 "
     model   vdw
     1.642 1.850
  nonbonded model="   0" pdb=" O   TYR A  89 "
            model="   0" pdb=" H   LYS A 101 "
     model   vdw
     1.734 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.742 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.809 1.850
  ... (remaining 30405 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: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (41.45, 74.18, 56.915, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (65.026, 54.011, 53.313, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 0.90, per 1000 atoms: 0.41
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (73.196, 44.547, 49.985, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  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, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  3.178)
  Mean delta:    0.011 (Z=  0.609)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.124 (Z=  4.000)
  Mean delta:    1.558 (Z=  0.859)

                      ----------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   153.69    26.31  5.00e+00  2.77e+01   5.3*sigma

  Min. delta:    0.021
  Max. delta:   84.950
  Mean delta:   12.818

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.203
  Mean delta:    0.075

                       ----------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            0.114       0.092      261.84   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.114
  Mean delta:    0.013

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.041   2241  Z= 0.433
    Angle     :  1.521   6.371   4077  Z= 0.659
    Chirality :  0.075   0.203    176
    Planarity :  0.010   0.108    326
    Dihedral  : 11.388  84.950    768
    Min Nonbonded Distance : 1.582
  
  Molprobity Statistics.
    All-atom Clashscore : 9.92
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      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:  0.49 (0.69), residues: 137
    helix:  0.11 (0.48), residues: 91
    sheet: -0.78 (1.84), residues: 10
    loop :  1.88 (1.16), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.017   0.004   PHE A  67 
   TYR   0.245   0.019   TYR A  81 
   ARG   0.037   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.200   0.023   TYR A  81 
   ARG   0.003   0.001   ARG A 129 

                     ----------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: 5
        1.23 -     1.42: 459
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.303  0.026 1.40e-02 5.10e+03 3.40e+00
  bond model="   0" pdb=" C   LEU A   3 "
       model="   0" pdb=" N   ILE A   4 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.53e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.361  0.017 1.10e-02 8.26e+03 2.31e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.05e+00
  bond model="   0" pdb=" C   GLU A 133 "
       model="   0" pdb=" N   HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.57e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.68 -   106.77: 70
      106.77 -   112.86: 2692
      112.86 -   118.95: 438
      118.95 -   125.04: 834
      125.04 -   131.13: 43
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" NE  ARG A 127 "
        model="   0" pdb=" CZ  ARG A 127 "
        model="   0" pdb=" NH1 ARG A 127 "
      ideal   model   delta    sigma   weight residual
     121.50  119.57    1.93 1.00e+00 1.00e+00 3.72e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.68    5.32 3.00e+00 1.11e-01 3.15e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.82    5.18 3.00e+00 1.11e-01 2.98e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  114.07   -5.07 3.00e+00 1.11e-01 2.86e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.92   -4.92 3.00e+00 1.11e-01 2.69e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 996
       17.93 -    35.85: 24
       35.85 -    53.78: 9
       53.78 -    71.70: 1
       71.70 -    89.63: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   74.75  -74.75     1      3.00e+01 1.11e-03 7.86e+00
  dihedral model="   0" pdb=" CA  ASP A  88 "
           model="   0" pdb=" C   ASP A  88 "
           model="   0" pdb=" N   TYR A  89 "
           model="   0" pdb=" CA  TYR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -168.16  -11.84     0      5.00e+00 4.00e-02 5.61e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -90.37  -89.63     2      3.00e+01 1.11e-03 5.33e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 110
       0.028 -    0.056: 38
       0.056 -    0.084: 20
       0.084 -    0.112: 6
       0.112 -    0.140: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality model="   0" pdb=" CA  ILE A  71 "
            model="   0" pdb=" N   ILE A  71 "
            model="   0" pdb=" C   ILE A  71 "
            model="   0" pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.10 2.00e-01 2.50e+01 2.68e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.017 5.00e-02 4.00e+02   2.57e-02 1.05e+00
        model="   0" pdb=" N   PRO A   6 "    0.044 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "    0.009 2.00e-02 2.50e+03   7.91e-03 9.38e-01
        model="   0" pdb=" CD  GLN A  66 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.011 2.00e-02 2.50e+03   4.93e-03 7.28e-01
        model="   0" pdb=" CG  TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 241
        2.25 -     2.84: 5130
        2.84 -     3.42: 5698
        3.42 -     4.01: 7725
        4.01 -     4.60: 11630
  Nonbonded interactions: 30424
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.661 1.850
  nonbonded model="   0" pdb=" HG2 LYS A  85 "
            model="   0" pdb=" O   GLY A  87 "
     model   vdw
     1.682 2.620
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.698 1.850
  nonbonded model="   0" pdb=" O   TYR A  89 "
            model="   0" pdb=" H   LYS A 101 "
     model   vdw
     1.702 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.757 1.850
  ... (remaining 30419 not shown)

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

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   9.92
  RMS(bonds)            =   0.0081
  RMS(angles)           =   1.52
  MolProbity score      =   2.21

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (48.269, 71.76, 56.823, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (53.918, 76.733, 46.869, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (59.017, 54.387, 61.257, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.06, per 1000 atoms: 0.48
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (74.598, 44.751, 35.044, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

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

  Time building chain proxies: 0.66, per 1000 atoms: 0.30
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (51.361, 56.97, 62.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 88
        1.23 -     1.43: 383
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.385 -0.031 1.10e-02 8.26e+03 7.95e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.68e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.59e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.69e+00
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.399 -0.025 1.10e-02 8.26e+03 5.07e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.46 -   106.22: 101
      106.22 -   111.98: 2513
      111.98 -   117.74: 467
      117.74 -   123.51: 863
      123.51 -   129.27: 133
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.51    4.69 1.30e+00 5.92e-01 1.30e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.52    4.68 1.30e+00 5.92e-01 1.30e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.02    3.58 1.00e+00 1.00e+00 1.28e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.65    4.55 1.30e+00 5.92e-01 1.23e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.27   -4.87 1.40e+00 5.10e-01 1.21e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 974
       16.44 -    32.88: 32
       32.88 -    49.32: 22
       49.32 -    65.75: 3
       65.75 -    82.19: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.20   30.80     0      5.00e+00 4.00e-02 3.79e+01
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.16   15.84     0      5.00e+00 4.00e-02 1.00e+01
  dihedral model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" CB  HIS A 138 "
           model="   0" pdb=" CG  HIS A 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.92   47.92     3      1.50e+01 4.44e-03 8.56e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 82
       0.046 -    0.091: 52
       0.091 -    0.136: 29
       0.136 -    0.181: 11
       0.181 -    0.227: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.72e-01
  chirality model="   0" pdb=" CA  SER A  90 "
            model="   0" pdb=" N   SER A  90 "
            model="   0" pdb=" C   SER A  90 "
            model="   0" pdb=" CB  SER A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.85e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.059 2.00e-02 2.50e+03   2.33e-02 1.63e+01
        model="   0" pdb=" CG  TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.057 2.00e-02 2.50e+03   2.25e-02 1.52e+01
        model="   0" pdb=" CG  TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.046 2.00e-02 2.50e+03   2.02e-02 1.23e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.004 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.20: 169
        2.20 -     2.80: 4418
        2.80 -     3.40: 6011
        3.40 -     4.00: 7313
        4.00 -     4.60: 11112
  Nonbonded interactions: 29023
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE1 GLU A  49 "
            model="   0" pdb=" HZ1 LYS A 125 "
     model   vdw
     1.606 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.681 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.714 1.850
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HG  SER A  90 "
     model   vdw
     1.733 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.749 1.850
  ... (remaining 29018 not shown)

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

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.58
  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: 0.80, per 1000 atoms: 0.36
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (41.366, 82.339, 49.673, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 9
        1.23 -     1.42: 455
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.40e-02 5.10e+03 2.64e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.362  0.016 1.10e-02 8.26e+03 2.06e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" CD2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.354  1.339  0.015 1.10e-02 8.26e+03 1.82e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.67e+00
  bond model="   0" pdb=" CD  ARG A  21 "
       model="   0" pdb=" NE  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.458  1.442  0.016 1.40e-02 5.10e+03 1.37e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   106.61: 64
      106.61 -   112.67: 2683
      112.67 -   118.74: 438
      118.74 -   124.80: 839
      124.80 -   130.87: 53
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.69    5.31 3.00e+00 1.11e-01 3.13e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.82    5.18 3.00e+00 1.11e-01 2.98e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.10   -5.10 3.00e+00 1.11e-01 2.89e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  105.06    4.94 3.00e+00 1.11e-01 2.71e+00
  angle model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" N   LYS A 109 "
      ideal   model   delta    sigma   weight residual
     116.20  119.46   -3.26 2.00e+00 2.50e-01 2.65e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 988
       17.28 -    34.56: 24
       34.56 -    51.83: 12
       51.83 -    69.11: 5
       69.11 -    86.39: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.39   86.39     1      3.00e+01 1.11e-03 9.99e+00
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" CB  LYS A  79 "
           model="   0" pdb=" CG  LYS A  79 "
           model="   0" pdb=" CD  LYS A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -131.77  -48.23     3      1.50e+01 4.44e-03 8.61e+00
  dihedral model="   0" pdb=" CA  TYR A  91 "
           model="   0" pdb=" C   TYR A  91 "
           model="   0" pdb=" N   THR A  92 "
           model="   0" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.39   14.61     0      5.00e+00 4.00e-02 8.54e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 108
       0.030 -    0.060: 39
       0.060 -    0.090: 23
       0.090 -    0.120: 4
       0.120 -    0.150: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  chirality model="   0" pdb=" CA  TYR A  89 "
            model="   0" pdb=" N   TYR A  89 "
            model="   0" pdb=" C   TYR A  89 "
            model="   0" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.21e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.017 5.00e-02 4.00e+02   2.64e-02 1.11e+00
        model="   0" pdb=" N   PRO A   6 "    0.046 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.015 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.013 2.00e-02 2.50e+03   5.48e-03 9.00e-01
        model="   0" pdb=" CG  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "   -0.008 2.00e-02 2.50e+03   7.28e-03 7.95e-01
        model="   0" pdb=" CD  GLN A  66 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 140
        2.17 -     2.78: 4463
        2.78 -     3.39: 6097
        3.39 -     3.99: 7738
        3.99 -     4.60: 11957
  Nonbonded interactions: 30395
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.565 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.627 1.850
  nonbonded model="   0" pdb=" HB  THR A  83 "
            model="   0" pdb=" O   THR A  92 "
     model   vdw
     1.756 2.620
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" HB3 SER A  46 "
     model   vdw
     1.792 2.440
  nonbonded model="   0" pdb=" HE2 LYS A  85 "
            model="   0" pdb=" O   GLY A  87 "
     model   vdw
     1.827 2.620
  ... (remaining 30390 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (43.085, 64.992, 58.034, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  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: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 105
        1.23 -     1.43: 366
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 134 "
       model="   0" pdb=" CE1 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.35e+01
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.32e+01
  bond model="   0" pdb=" NE  ARG A  58 "
       model="   0" pdb=" CZ  ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.326  1.366 -0.040 1.10e-02 8.26e+03 1.31e+01
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.29e+01
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.29e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       93.17 -   101.07: 6
      101.07 -   108.97: 934
      108.97 -   116.88: 2123
      116.88 -   124.78: 958
      124.78 -   132.68: 56
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  105.91    7.89 1.00e+00 1.00e+00 6.23e+01
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  101.41   12.49 1.80e+00 3.09e-01 4.82e+01
  angle model="   0" pdb=" CA  ASP A  47 "
        model="   0" pdb=" CB  ASP A  47 "
        model="   0" pdb=" CG  ASP A  47 "
      ideal   model   delta    sigma   weight residual
     112.60  106.06    6.54 1.00e+00 1.00e+00 4.28e+01
  angle model="   0" pdb=" C   ASP A 110 "
        model="   0" pdb=" N   TYR A 111 "
        model="   0" pdb=" CA  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     121.70  132.68  -10.98 1.80e+00 3.09e-01 3.72e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" CB  ASP A 118 "
        model="   0" pdb=" CG  ASP A 118 "
      ideal   model   delta    sigma   weight residual
     112.60  106.59    6.01 1.00e+00 1.00e+00 3.61e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 966
       17.92 -    35.84: 48
       35.84 -    53.76: 8
       53.76 -    71.69: 8
       71.69 -    89.61: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" C   ILE A  77 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
           model="   0" pdb=" CB  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -112.22   -9.78     0      2.50e+00 1.60e-01 1.53e+01
  dihedral model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   ILE A  51 "
           model="   0" pdb=" CA  ILE A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.11  -17.89     0      5.00e+00 4.00e-02 1.28e+01
  dihedral model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.20    8.60     0      2.50e+00 1.60e-01 1.18e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 142
       0.094 -    0.188: 21
       0.188 -    0.283: 10
       0.283 -    0.377: 2
       0.377 -    0.471: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.54e+00
  chirality model="   0" pdb=" CA  PRO A 117 "
            model="   0" pdb=" N   PRO A 117 "
            model="   0" pdb=" C   PRO A 117 "
            model="   0" pdb=" CB  PRO A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.31 2.00e-01 2.50e+01 2.43e+00
  chirality model="   0" pdb=" CA  TYR A 111 "
            model="   0" pdb=" N   TYR A 111 "
            model="   0" pdb=" C   TYR A 111 "
            model="   0" pdb=" CB  TYR A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.17e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ASP A 116 "    0.055 5.00e-02 4.00e+02   8.33e-02 1.11e+01
        model="   0" pdb=" N   PRO A 117 "   -0.144 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A 117 "    0.046 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A 117 "    0.043 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "    0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        model="   0" pdb=" N   PRO A  54 "   -0.139 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "    0.043 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "    0.043 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  ILE A  71 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        model="   0" pdb=" C   ILE A  71 "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" O   ILE A  71 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" N   ASN A  72 "    0.018 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.12 -     1.82: 42
        1.82 -     2.51: 1872
        2.51 -     3.21: 7226
        3.21 -     3.90: 8011
        3.90 -     4.60: 12781
  Nonbonded interactions: 29932
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  78 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.122 2.270
  nonbonded model="   0" pdb="HD13 ILE A 131 "
            model="   0" pdb=" HB2 HIS A 134 "
     model   vdw
     1.209 2.440
  nonbonded model="   0" pdb="HD11 LEU A  93 "
            model="   0" pdb=" HB2 LEU A  99 "
     model   vdw
     1.303 2.440
  nonbonded model="   0" pdb="HG22 THR A  83 "
            model="   0" pdb=" H   GLU A  84 "
     model   vdw
     1.322 2.270
  nonbonded model="   0" pdb="HD22 LEU A   2 "
            model="   0" pdb=" HG  LEU A  61 "
     model   vdw
     1.331 2.440
  ... (remaining 29927 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 5
        1.23 -     1.42: 459
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.024 1.40e-02 5.10e+03 2.97e+00
  bond model="   0" pdb=" C   LYS A  85 "
       model="   0" pdb=" N   ILE A  86 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.31e+00
  bond model="   0" pdb=" C   GLY A  73 "
       model="   0" pdb=" N   ASP A  74 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.77e+00
  bond model="   0" pdb=" C   GLN A 100 "
       model="   0" pdb=" N   LYS A 101 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.68e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.313  0.017 1.30e-02 5.92e+03 1.64e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.03 -   106.24: 45
      106.24 -   112.46: 2690
      112.46 -   118.68: 449
      118.68 -   124.89: 847
      124.89 -   131.11: 46
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.53    5.47 3.00e+00 1.11e-01 3.32e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.36   -5.36 3.00e+00 1.11e-01 3.19e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.70    5.30 3.00e+00 1.11e-01 3.13e+00
  angle model="   0" pdb=" C   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  103.83    5.17 3.00e+00 1.11e-01 2.97e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  105.07    4.93 3.00e+00 1.11e-01 2.70e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 999
       17.27 -    34.55: 19
       34.55 -    51.82: 8
       51.82 -    69.09: 3
       69.09 -    86.37: 3
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.80   84.80     1      3.00e+01 1.11e-03 9.70e+00
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -81.60   81.60     1      3.00e+01 1.11e-03 9.11e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -93.63  -86.37     2      3.00e+01 1.11e-03 5.31e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 102
       0.026 -    0.052: 44
       0.052 -    0.079: 18
       0.079 -    0.105: 10
       0.105 -    0.131: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.29e-01
  chirality model="   0" pdb=" CA  ASP A  44 "
            model="   0" pdb=" N   ASP A  44 "
            model="   0" pdb=" C   ASP A  44 "
            model="   0" pdb=" CB  ASP A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.93e-01
  chirality model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.55e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.017 5.00e-02 4.00e+02   2.64e-02 1.12e+00
        model="   0" pdb=" N   PRO A   6 "   -0.046 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.015 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.015 2.00e-02 2.50e+03   5.75e-03 9.92e-01
        model="   0" pdb=" CG  TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "   -0.008 2.00e-02 2.50e+03   6.74e-03 6.81e-01
        model="   0" pdb=" CD  GLN A  66 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.08 -     1.79: 3
        1.79 -     2.49: 1530
        2.49 -     3.19: 7006
        3.19 -     3.90: 8322
        3.90 -     4.60: 13351
  Nonbonded interactions: 30212
  Sorted by model distance:
  nonbonded model="   0" pdb="HD13 ILE A  71 "
            model="   0" pdb=" HE1 TYR A  91 "
     model   vdw
     1.083 2.270
  nonbonded model="   0" pdb=" HZ  PHE A  67 "
            model="   0" pdb=" O   TYR A  89 "
     model   vdw
     1.710 2.450
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.734 1.850
  nonbonded model="   0" pdb=" HE1 TYR A  68 "
            model="   0" pdb=" HE1 TYR A  89 "
     model   vdw
     1.807 2.100
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.829 1.850
  ... (remaining 30207 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: 136
        1.23 -     1.43: 338
        1.43 -     1.62: 657
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" NE  ARG A 129 "
       model="   0" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.37e+01
  bond model="   0" pdb=" ND1 HIS A 134 "
       model="   0" pdb=" CE1 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.37e+01
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.34e+01
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.33e+01
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.30e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       94.92 -   103.46: 30
      103.46 -   112.00: 2507
      112.00 -   120.53: 987
      120.53 -   129.07: 538
      129.07 -   137.61: 15
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   ILE A 131 "
        model="   0" pdb=" N   LEU A 132 "
        model="   0" pdb=" CA  LEU A 132 "
      ideal   model   delta    sigma   weight residual
     121.70  137.61  -15.91 1.80e+00 3.09e-01 7.81e+01
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  100.61   13.29 1.80e+00 3.09e-01 5.45e+01
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  107.03    6.77 1.00e+00 1.00e+00 4.58e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" CB  ASP A 118 "
        model="   0" pdb=" CG  ASP A 118 "
      ideal   model   delta    sigma   weight residual
     112.60  106.28    6.32 1.00e+00 1.00e+00 4.00e+01
  angle model="   0" pdb=" C   GLU A  49 "
        model="   0" pdb=" N   TYR A  50 "
        model="   0" pdb=" CA  TYR A  50 "
      ideal   model   delta    sigma   weight residual
     121.70  132.49  -10.79 1.80e+00 3.09e-01 3.59e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.01: 910
       12.01 -    24.02: 81
       24.02 -    36.03: 29
       36.03 -    48.04: 6
       48.04 -    60.05: 6
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LEU A 132 "
           model="   0" pdb=" C   LEU A 132 "
           model="   0" pdb=" N   GLU A 133 "
           model="   0" pdb=" CA  GLU A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.48  -31.52     0      5.00e+00 4.00e-02 3.98e+01
  dihedral model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.42    8.82     0      2.50e+00 1.60e-01 1.25e+01
  dihedral model="   0" pdb=" CA  GLY A  73 "
           model="   0" pdb=" C   GLY A  73 "
           model="   0" pdb=" N   ASP A  74 "
           model="   0" pdb=" CA  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.41  -17.59     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 116
       0.090 -    0.179: 41
       0.179 -    0.268: 12
       0.268 -    0.358: 5
       0.358 -    0.447: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 4.99e+00
  chirality model="   0" pdb=" CA  TYR A 111 "
            model="   0" pdb=" N   TYR A 111 "
            model="   0" pdb=" C   TYR A 111 "
            model="   0" pdb=" CB  TYR A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.37e+00
  chirality model="   0" pdb=" CA  PRO A   6 "
            model="   0" pdb=" N   PRO A   6 "
            model="   0" pdb=" C   PRO A   6 "
            model="   0" pdb=" CB  PRO A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.07e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "    0.065 5.00e-02 4.00e+02   9.90e-02 1.57e+01
        model="   0" pdb=" N   PRO A  54 "   -0.171 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "    0.054 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "    0.052 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ILE A  51 "    0.062 5.00e-02 4.00e+02   9.39e-02 1.41e+01
        model="   0" pdb=" N   PRO A  52 "   -0.162 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  52 "    0.049 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  52 "    0.052 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  ILE A  71 "    0.017 2.00e-02 2.50e+03   3.35e-02 1.12e+01
        model="   0" pdb=" C   ILE A  71 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" O   ILE A  71 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" N   ASN A  72 "    0.019 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.11 -     1.81: 32
        1.81 -     2.51: 1811
        2.51 -     3.20: 7189
        3.20 -     3.90: 8093
        3.90 -     4.60: 12865
  Nonbonded interactions: 29990
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 LEU A   2 "
            model="   0" pdb=" HG  LEU A  61 "
     model   vdw
     1.111 2.440
  nonbonded model="   0" pdb=" HG2 PRO A  22 "
            model="   0" pdb="HD13 LEU A  25 "
     model   vdw
     1.185 2.440
  nonbonded model="   0" pdb="HG22 THR A  83 "
            model="   0" pdb=" H   GLU A  84 "
     model   vdw
     1.374 2.270
  nonbonded model="   0" pdb=" HD3 LYS A 125 "
            model="   0" pdb=" HD2 ARG A 129 "
     model   vdw
     1.382 2.440
  nonbonded model="   0" pdb=" HG2 PRO A 117 "
            model="   0" pdb="HD12 LEU A 119 "
     model   vdw
     1.408 2.440
  ... (remaining 29985 not shown)

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.69 seconds

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

  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (53.333, 63.115, 57.439, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     216      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  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: 1.10
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 461
        1.42 -     1.61: 670
        1.61 -     1.80: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   PRO A 102 "
       model="   0" pdb=" N   ASP A 103 "
    ideal  model  delta    sigma   weight residual
    1.329  1.301  0.028 1.40e-02 5.10e+03 4.12e+00
  bond model="   0" pdb=" C   HIS A 136 "
       model="   0" pdb=" N   HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.301  0.028 1.40e-02 5.10e+03 4.01e+00
  bond model="   0" pdb=" C   LYS A  85 "
       model="   0" pdb=" N   ILE A  86 "
    ideal  model  delta    sigma   weight residual
    1.329  1.303  0.026 1.40e-02 5.10e+03 3.54e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.303  0.026 1.40e-02 5.10e+03 3.40e+00
  bond model="   0" pdb=" C   THR A  20 "
       model="   0" pdb=" N   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.329  1.304  0.025 1.40e-02 5.10e+03 3.08e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.25 -   106.50: 54
      106.50 -   112.75: 2703
      112.75 -   119.00: 446
      119.00 -   125.26: 831
      125.26 -   131.51: 43
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.43    5.57 3.00e+00 1.11e-01 3.45e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.76    5.24 3.00e+00 1.11e-01 3.05e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.19   -5.19 3.00e+00 1.11e-01 2.99e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  114.17   -5.17 3.00e+00 1.11e-01 2.97e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  104.84    5.16 3.00e+00 1.11e-01 2.96e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 990
       17.42 -    34.84: 20
       34.84 -    52.26: 16
       52.26 -    69.67: 2
       69.67 -    87.09: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.98  -85.98     1      3.00e+01 1.11e-03 9.92e+00
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -81.42   81.42     1      3.00e+01 1.11e-03 9.08e+00
  dihedral model="   0" pdb=" CB  GLU A 120 "
           model="   0" pdb=" CG  GLU A 120 "
           model="   0" pdb=" CD  GLU A 120 "
           model="   0" pdb=" OE1 GLU A 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.24   78.24     1      3.00e+01 1.11e-03 8.49e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 83
       0.025 -    0.050: 52
       0.050 -    0.074: 25
       0.074 -    0.099: 9
       0.099 -    0.123: 7
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality model="   0" pdb=" CA  TYR A  89 "
            model="   0" pdb=" N   TYR A  89 "
            model="   0" pdb=" C   TYR A  89 "
            model="   0" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.94e-01
  chirality model="   0" pdb=" CA  VAL A 112 "
            model="   0" pdb=" N   VAL A 112 "
            model="   0" pdb=" C   VAL A 112 "
            model="   0" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 2.90e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.017 5.00e-02 4.00e+02   2.59e-02 1.07e+00
        model="   0" pdb=" N   PRO A   6 "   -0.045 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.013 2.00e-02 2.50e+03   5.09e-03 7.77e-01
        model="   0" pdb=" CG  TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ASP A 116 "   -0.014 5.00e-02 4.00e+02   2.17e-02 7.52e-01
        model="   0" pdb=" N   PRO A 117 "    0.037 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A 117 "   -0.011 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A 117 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.10: 81
        2.10 -     2.73: 3945
        2.73 -     3.35: 6288
        3.35 -     3.98: 7812
        3.98 -     4.60: 12102
  Nonbonded interactions: 30228
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.475 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.499 1.850
  nonbonded model="   0" pdb=" HE3 LYS A  85 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.544 2.270
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" HB3 SER A  46 "
     model   vdw
     1.567 2.440
  nonbonded model="   0" pdb=" O   TYR A  89 "
            model="   0" pdb=" H   LYS A 101 "
     model   vdw
     1.632 1.850
  ... (remaining 30223 not shown)

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

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

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

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 135
        1.23 -     1.43: 341
        1.43 -     1.62: 655
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.43e+01
  bond model="   0" pdb=" NE  ARG A  58 "
       model="   0" pdb=" CZ  ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.37e+01
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.32e+01
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.27e+01
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.27e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       94.56 -   102.11: 9
      102.11 -   109.67: 1883
      109.67 -   117.23: 1201
      117.23 -   124.79: 923
      124.79 -   132.35: 61
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  100.97   12.93 1.80e+00 3.09e-01 5.16e+01
  angle model="   0" pdb=" CA  ASP A  95 "
        model="   0" pdb=" CB  ASP A  95 "
        model="   0" pdb=" CG  ASP A  95 "
      ideal   model   delta    sigma   weight residual
     112.60  106.14    6.46 1.00e+00 1.00e+00 4.18e+01
  angle model="   0" pdb=" CA  ASP A   7 "
        model="   0" pdb=" CB  ASP A   7 "
        model="   0" pdb=" CG  ASP A   7 "
      ideal   model   delta    sigma   weight residual
     112.60  106.34    6.26 1.00e+00 1.00e+00 3.92e+01
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  107.56    6.24 1.00e+00 1.00e+00 3.90e+01
  angle model="   0" pdb=" C   GLY A  94 "
        model="   0" pdb=" N   ASP A  95 "
        model="   0" pdb=" CA  ASP A  95 "
      ideal   model   delta    sigma   weight residual
     121.70  111.02   10.68 1.80e+00 3.09e-01 3.52e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.40: 942
       14.40 -    28.79: 63
       28.79 -    43.19: 15
       43.19 -    57.58: 8
       57.58 -    71.98: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" CB  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.01   10.79     0      2.50e+00 1.60e-01 1.86e+01
  dihedral model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.63   10.03     0      2.50e+00 1.60e-01 1.61e+01
  dihedral model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.78   -9.98     0      2.50e+00 1.60e-01 1.59e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 126
       0.104 -    0.207: 37
       0.207 -    0.311: 10
       0.311 -    0.414: 2
       0.414 -    0.518: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.71e+00
  chirality model="   0" pdb=" CA  PRO A   6 "
            model="   0" pdb=" N   PRO A   6 "
            model="   0" pdb=" C   PRO A   6 "
            model="   0" pdb=" CB  PRO A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.35    0.37 2.00e-01 2.50e+01 3.47e+00
  chirality model="   0" pdb=" CA  TYR A 111 "
            model="   0" pdb=" N   TYR A 111 "
            model="   0" pdb=" C   TYR A 111 "
            model="   0" pdb=" CB  TYR A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.17e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LYS A 113 "    0.058 5.00e-02 4.00e+02   8.90e-02 1.27e+01
        model="   0" pdb=" N   PRO A 114 "   -0.154 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A 114 "    0.048 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A 114 "    0.048 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  TYR A 111 "   -0.016 2.00e-02 2.50e+03   3.11e-02 9.66e+00
        model="   0" pdb=" C   TYR A 111 "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" O   TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" N   VAL A 112 "   -0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  GLU A  49 "    0.015 2.00e-02 2.50e+03   3.02e-02 9.13e+00
        model="   0" pdb=" C   GLU A  49 "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" O   GLU A  49 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" N   TYR A  50 "    0.017 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.11 -     1.81: 43
        1.81 -     2.51: 1876
        2.51 -     3.21: 7161
        3.21 -     3.90: 8113
        3.90 -     4.60: 12738
  Nonbonded interactions: 29931
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  78 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.114 2.270
  nonbonded model="   0" pdb="HD23 LEU A   2 "
            model="   0" pdb="HD13 LEU A  61 "
     model   vdw
     1.130 2.440
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD11 ILE A  77 "
     model   vdw
     1.273 2.440
  nonbonded model="   0" pdb=" HA  VAL A  41 "
            model="   0" pdb="HG23 VAL A 112 "
     model   vdw
     1.283 2.440
  nonbonded model="   0" pdb=" H   LYS A  79 "
            model="   0" pdb=" HD2 LYS A  79 "
     model   vdw
     1.317 2.270
  ... (remaining 29926 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 124
        1.23 -     1.43: 347
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.48e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.386 -0.032 1.10e-02 8.26e+03 8.40e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.27e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 7.01e+00
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.96e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.48 -   106.23: 107
      106.23 -   111.97: 2508
      111.97 -   117.72: 477
      117.72 -   123.47: 837
      123.47 -   129.21: 148
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.66    3.94 1.00e+00 1.00e+00 1.55e+01
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.90    3.70 1.00e+00 1.00e+00 1.37e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.41    4.79 1.30e+00 5.92e-01 1.36e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.42    4.78 1.30e+00 5.92e-01 1.35e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.21   -4.81 1.40e+00 5.10e-01 1.18e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 965
       16.97 -    33.95: 47
       33.95 -    50.92: 17
       50.92 -    67.89: 2
       67.89 -    84.86: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.14   34.86     0      5.00e+00 4.00e-02 4.86e+01
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.38   27.62     0      5.00e+00 4.00e-02 3.05e+01
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.58   26.42     0      5.00e+00 4.00e-02 2.79e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 69
       0.038 -    0.076: 49
       0.076 -    0.113: 29
       0.113 -    0.151: 25
       0.151 -    0.189: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.92e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.48e-01
  chirality model="   0" pdb=" CG  LEU A  53 "
            model="   0" pdb=" CB  LEU A  53 "
            model="   0" pdb=" CD1 LEU A  53 "
            model="   0" pdb=" CD2 LEU A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.064 2.00e-02 2.50e+03   2.77e-02 2.30e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.062 2.00e-02 2.50e+03   2.34e-02 1.65e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.053 2.00e-02 2.50e+03   2.23e-02 1.50e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 178
        2.21 -     2.81: 4472
        2.81 -     3.40: 5959
        3.40 -     4.00: 7424
        4.00 -     4.60: 11156
  Nonbonded interactions: 29189
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.610 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.704 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.709 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.778 1.850
  ... (remaining 29184 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.042 (Z=  2.663)
  Mean delta:    0.012 (Z=  0.612)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   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=  0.001)
  Max. delta:    6.060 (Z=  4.110)
  Mean delta:    1.587 (Z=  0.867)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   151.52    28.48  5.00e+00  3.24e+01   5.7*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   151.94    28.06  5.00e+00  3.15e+01   5.6*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   152.43    27.57  5.00e+00  3.04e+01   5.5*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   153.83    26.17  5.00e+00  2.74e+01   5.2*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   155.53    24.47  5.00e+00  2.40e+01   4.9*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   157.14    22.86  5.00e+00  2.09e+01   4.6*sigma

  Min. delta:    0.003
  Max. delta:   85.099
  Mean delta:   12.519

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.203
  Mean delta:    0.075

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.042   2241  Z= 0.436
    Angle     :  1.530   6.060   4077  Z= 0.662
    Chirality :  0.075   0.203    176
    Planarity :  0.007   0.034    326
    Dihedral  : 11.312  85.977    768
    Min Nonbonded Distance : 1.683
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  3.65 %
      Favored  : 94.89 %
    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: -0.79 (0.68), residues: 137
    helix: -0.47 (0.48), residues: 82
    sheet: -1.32 (1.53), residues: 10
    loop : -0.03 (1.07), residues: 45
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS A 139 
   PHE   0.017   0.004   PHE A  45 
   TYR   0.061   0.010   TYR A 111 
   ARG   0.039   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS A 139 
   PHE   0.013   0.005   PHE A  67 
   TYR   0.052   0.011   TYR A 111 
   ARG   0.006   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 36
        1.23 -     1.42: 428
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 135 "
       model="   0" pdb=" N   HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.329  1.304  0.025 1.40e-02 5.10e+03 3.07e+00
  bond model="   0" pdb=" C   LYS A  79 "
       model="   0" pdb=" N   GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.38e+00
  bond model="   0" pdb=" C   GLU A  84 "
       model="   0" pdb=" N   LYS A  85 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.03e+00
  bond model="   0" pdb=" C   LYS A 113 "
       model="   0" pdb=" N   PRO A 114 "
    ideal  model  delta    sigma   weight residual
    1.341  1.319  0.022 1.60e-02 3.91e+03 1.83e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.61e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.32 -   106.58: 85
      106.58 -   112.84: 2662
      112.84 -   119.10: 459
      119.10 -   125.36: 829
      125.36 -   131.62: 42
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" N   ASP A 103 "
        model="   0" pdb=" CA  ASP A 103 "
        model="   0" pdb=" C   ASP A 103 "
      ideal   model   delta    sigma   weight residual
     111.00  104.59    6.41 2.80e+00 1.28e-01 5.24e+00
  angle model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" CB  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     111.60  107.35    4.25 2.00e+00 2.50e-01 4.52e+00
  angle model="   0" pdb=" N   VAL A  41 "
        model="   0" pdb=" CA  VAL A  41 "
        model="   0" pdb=" HA  VAL A  41 "
      ideal   model   delta    sigma   weight residual
     110.00  103.70    6.30 3.00e+00 1.11e-01 4.41e+00
  angle model="   0" pdb=" C   PRO A 102 "
        model="   0" pdb=" CA  PRO A 102 "
        model="   0" pdb=" HA  PRO A 102 "
      ideal   model   delta    sigma   weight residual
     109.00  102.73    6.27 3.00e+00 1.11e-01 4.37e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  103.98    6.02 3.00e+00 1.11e-01 4.02e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 981
       16.72 -    33.44: 30
       33.44 -    50.16: 12
       50.16 -    66.88: 5
       66.88 -    83.59: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.59  -83.59     1      3.00e+01 1.11e-03 9.48e+00
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   69.96  -69.96     1      3.00e+01 1.11e-03 7.01e+00
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   63.45  -63.45     1      3.00e+01 1.11e-03 5.90e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.050: 94
       0.050 -    0.100: 60
       0.100 -    0.150: 15
       0.150 -    0.199: 4
       0.199 -    0.249: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.052 2.00e-02 2.50e+03   1.96e-02 1.16e+01
        model="   0" pdb=" CG  TYR A 111 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 105 "   -0.033 2.00e-02 2.50e+03   1.28e-02 4.88e+00
        model="   0" pdb=" CG  TYR A 105 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 105 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 105 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 105 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 105 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 105 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 105 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 105 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 105 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 105 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 105 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.030 2.00e-02 2.50e+03   1.17e-02 4.10e+00
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.11: 73
        2.11 -     2.73: 4021
        2.73 -     3.35: 6210
        3.35 -     3.98: 7763
        3.98 -     4.60: 11916
  Nonbonded interactions: 29983
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.482 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.581 1.850
  nonbonded model="   0" pdb="HG12 VAL A 112 "
            model="   0" pdb=" HD3 PRO A 114 "
     model   vdw
     1.585 2.440
  nonbonded model="   0" pdb=" HE  ARG A  21 "
            model="   0" pdb=" OD2 ASP A  29 "
     model   vdw
     1.722 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.751 1.850
  ... (remaining 29978 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   1.46 %
                favored =  94.89 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.53
  MolProbity score      =   1.80

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  1.259)
  Mean delta:    0.004 (Z=  0.220)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    3.948 (Z=  1.436)
  Mean delta:    0.828 (Z=  0.399)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.016
  Max. delta:   79.682
  Mean delta:   10.579

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.133
  Mean delta:    0.040

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.003

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.022   2241  Z= 0.157
    Angle     :  1.135   5.539   4077  Z= 0.418
    Chirality :  0.040   0.133    176
    Planarity :  0.003   0.026    326
    Dihedral  :  9.740  79.682    768
    Min Nonbonded Distance : 1.261
  
  Molprobity Statistics.
    All-atom Clashscore : 15.79
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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:  1.48 (0.70), residues: 137
    helix:  1.14 (0.52), residues: 87
    sheet: -0.14 (1.97), residues: 10
    loop :  1.30 (1.01), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A  43 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.012   0.002   TYR A 111 
   ARG   0.012   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A  43 
   PHE   0.001   0.000   PHE A  67 
   TYR   0.012   0.002   TYR A 111 
   ARG   0.003   0.001   ARG A 127 

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

   A 139  HIS
   A  66  GLN
   A 138  HIS

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

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  15.79
  RMS(bonds)            =   0.0028
  RMS(angles)           =   1.13
  MolProbity score      =   1.70

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: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 3
        1.23 -     1.42: 461
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.40e-02 5.10e+03 2.68e+00
  bond model="   0" pdb=" C   LYS A 101 "
       model="   0" pdb=" N   PRO A 102 "
    ideal  model  delta    sigma   weight residual
    1.341  1.318  0.023 1.60e-02 3.91e+03 2.00e+00
  bond model="   0" pdb=" CG  HIS A 139 "
       model="   0" pdb=" ND1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.378  1.364  0.014 1.10e-02 8.26e+03 1.64e+00
  bond model="   0" pdb=" C   TYR A  81 "
       model="   0" pdb=" N   THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.63e+00
  bond model="   0" pdb=" C   VAL A  41 "
       model="   0" pdb=" N   GLY A  42 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.44e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.33 -   106.52: 58
      106.52 -   112.71: 2692
      112.71 -   118.90: 448
      118.90 -   125.08: 835
      125.08 -   131.27: 44
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" C   TYR A  81 "
        model="   0" pdb=" N   THR A  82 "
        model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta    sigma   weight residual
     121.70  126.79   -5.09 1.80e+00 3.09e-01 7.99e+00
  angle model="   0" pdb=" N   THR A  82 "
        model="   0" pdb=" CA  THR A  82 "
        model="   0" pdb=" HA  THR A  82 "
      ideal   model   delta    sigma   weight residual
     110.00  103.72    6.28 3.00e+00 1.11e-01 4.38e+00
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.33   -5.33 3.00e+00 1.11e-01 3.15e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.70    5.30 3.00e+00 1.11e-01 3.12e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  104.91    5.09 3.00e+00 1.11e-01 2.88e+00
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 987
       17.62 -    35.23: 27
       35.23 -    52.85: 10
       52.85 -    70.46: 4
       70.46 -    88.08: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.91   86.91     1      3.00e+01 1.11e-03 1.01e+01
  dihedral model="   0" pdb=" CB  GLU A  84 "
           model="   0" pdb=" CG  GLU A  84 "
           model="   0" pdb=" CD  GLU A  84 "
           model="   0" pdb=" OE1 GLU A  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.13  -84.13     1      3.00e+01 1.11e-03 9.58e+00
  dihedral model="   0" pdb=" CA  TYR A  12 "
           model="   0" pdb=" C   TYR A  12 "
           model="   0" pdb=" N   SER A  13 "
           model="   0" pdb=" CA  SER A  13 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -167.69  -12.31     0      5.00e+00 4.00e-02 6.07e+00
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 130
       0.039 -    0.077: 35
       0.077 -    0.115: 8
       0.115 -    0.154: 2
       0.154 -    0.192: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" C   THR A  82 "
            model="   0" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.19 2.00e-01 2.50e+01 9.25e-01
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.79e-01
  chirality model="   0" pdb=" CA  VAL A 112 "
            model="   0" pdb=" N   VAL A 112 "
            model="   0" pdb=" C   VAL A 112 "
            model="   0" pdb=" CB  VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.017 2.00e-02 2.50e+03   7.02e-03 1.48e+00
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.017 5.00e-02 4.00e+02   2.58e-02 1.07e+00
        model="   0" pdb=" N   PRO A   6 "    0.045 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.015 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLN A  66 "   -0.010 2.00e-02 2.50e+03   8.26e-03 1.02e+00
        model="   0" pdb=" CD  GLN A  66 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLN A  66 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 GLN A  66 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb="HE21 GLN A  66 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb="HE22 GLN A  66 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 170
        2.20 -     2.80: 4627
        2.80 -     3.40: 6114
        3.40 -     4.00: 7623
        4.00 -     4.60: 11766
  Nonbonded interactions: 30300
  Sorted by model distance:
  nonbonded model="   0" pdb=" HD1 TYR A  81 "
            model="   0" pdb="HG23 THR A  82 "
     model   vdw
     1.603 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.628 1.850
  nonbonded model="   0" pdb=" O   TYR A  89 "
            model="   0" pdb=" H   LYS A 101 "
     model   vdw
     1.679 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.687 1.850
  nonbonded model="   0" pdb=" HG1 THR A  83 "
            model="   0" pdb=" O   THR A  92 "
     model   vdw
     1.727 1.850
  ... (remaining 30295 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: 1.08
  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 -     1.04: 1106
        1.04 -     1.23: 127
        1.23 -     1.43: 344
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.35e+01
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.34e+01
  bond model="   0" pdb=" NE  ARG A  21 "
       model="   0" pdb=" CZ  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.326  1.366 -0.040 1.10e-02 8.26e+03 1.34e+01
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.31e+01
  bond model="   0" pdb=" NE  ARG A 127 "
       model="   0" pdb=" CZ  ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.326  1.365 -0.039 1.10e-02 8.26e+03 1.28e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       95.32 -   102.89: 16
      102.89 -   110.47: 2183
      110.47 -   118.04: 959
      118.04 -   125.62: 892
      125.62 -   133.19: 27
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  106.76    7.04 1.00e+00 1.00e+00 4.96e+01
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  101.67   12.23 1.80e+00 3.09e-01 4.62e+01
  angle model="   0" pdb=" C   ASP A 110 "
        model="   0" pdb=" N   TYR A 111 "
        model="   0" pdb=" CA  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     121.70  133.19  -11.49 1.80e+00 3.09e-01 4.08e+01
  angle model="   0" pdb=" CA  ASP A   7 "
        model="   0" pdb=" CB  ASP A   7 "
        model="   0" pdb=" CG  ASP A   7 "
      ideal   model   delta    sigma   weight residual
     112.60  106.80    5.80 1.00e+00 1.00e+00 3.37e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  106.87    5.73 1.00e+00 1.00e+00 3.29e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.18: 963
       16.18 -    32.35: 51
       32.35 -    48.53: 9
       48.53 -    64.71: 7
       64.71 -    80.89: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.95    9.35     0      2.50e+00 1.60e-01 1.40e+01
  dihedral model="   0" pdb=" N   TYR A  50 "
           model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" CB  TYR A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.49   -8.69     0      2.50e+00 1.60e-01 1.21e+01
  dihedral model="   0" pdb=" CA  ASP A  44 "
           model="   0" pdb=" CB  ASP A  44 "
           model="   0" pdb=" CG  ASP A  44 "
           model="   0" pdb=" OD1 ASP A  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.47   59.47     1      2.00e+01 2.50e-03 1.18e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 135
       0.099 -    0.198: 28
       0.198 -    0.296: 10
       0.296 -    0.395: 2
       0.395 -    0.494: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.09e+00
  chirality model="   0" pdb=" CA  PRO A   6 "
            model="   0" pdb=" N   PRO A   6 "
            model="   0" pdb=" C   PRO A   6 "
            model="   0" pdb=" CB  PRO A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality model="   0" pdb=" CA  TYR A 111 "
            model="   0" pdb=" N   TYR A 111 "
            model="   0" pdb=" C   TYR A 111 "
            model="   0" pdb=" CB  TYR A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.93e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "    0.065 5.00e-02 4.00e+02   9.89e-02 1.56e+01
        model="   0" pdb=" N   PRO A  54 "   -0.171 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "    0.054 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "    0.052 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   ILE A  51 "    0.058 5.00e-02 4.00e+02   8.81e-02 1.24e+01
        model="   0" pdb=" N   PRO A  52 "   -0.152 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  52 "    0.046 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  52 "    0.049 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.056 5.00e-02 4.00e+02   8.62e-02 1.19e+01
        model="   0" pdb=" N   PRO A   6 "    0.149 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.047 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.31 -     1.97: 81
        1.97 -     2.63: 3029
        2.63 -     3.28: 6811
        3.28 -     3.94: 7748
        3.94 -     4.60: 12100
  Nonbonded interactions: 29769
  Sorted by model distance:
  nonbonded model="   0" pdb="HD12 LEU A   2 "
            model="   0" pdb=" H   ILE A   4 "
     model   vdw
     1.310 2.270
  nonbonded model="   0" pdb=" H   LYS A  79 "
            model="   0" pdb=" HD2 LYS A  79 "
     model   vdw
     1.327 2.270
  nonbonded model="   0" pdb="HD12 LEU A   2 "
            model="   0" pdb="HG12 ILE A   4 "
     model   vdw
     1.342 2.440
  nonbonded model="   0" pdb=" HB2 ASP A  47 "
            model="   0" pdb=" HB2 TYR A  50 "
     model   vdw
     1.388 2.440
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.445 2.270
  ... (remaining 29764 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  3.205)
  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   118.37     4.23  1.00e+00  1.79e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.353 (Z=  4.229)
  Mean delta:    1.631 (Z=  0.888)

                      ----------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   135.70    44.30  5.00e+00  7.85e+01   8.9*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   145.41    34.59  5.00e+00  4.79e+01   6.9*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   159.26    20.74  5.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.082
  Max. delta:   85.326
  Mean delta:   11.831

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.048
  Mean delta:    0.011

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2241  Z= 0.443
    Angle     :  1.561   7.353   4077  Z= 0.676
    Chirality :  0.076   0.204    176
    Planarity :  0.008   0.038    326
    Dihedral  : 10.707  85.326    768
    Min Nonbonded Distance : 1.307
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  2.92 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.81 %
      Favored  : 98.39 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 1.53 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.24 (0.71), residues: 137
    helix:  0.04 (0.49), residues: 87
    sheet: -1.64 (1.57), residues: 10
    loop :  1.47 (1.20), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.020   0.004   PHE A  45 
   TYR   0.068   0.011   TYR A  50 
   ARG   0.039   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.012   0.004   PHE A  45 
   TYR   0.057   0.013   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   2.92 %
                favored =  94.16 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.56
  MolProbity score      =   1.71

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

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

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

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 128
        1.23 -     1.43: 345
        1.43 -     1.62: 658
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.43e+01
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.358 -0.037 1.00e-02 1.00e+04 1.37e+01
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.32e+01
  bond model="   0" pdb=" ND1 HIS A 134 "
       model="   0" pdb=" CE1 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.32e+01
  bond model="   0" pdb=" NE  ARG A  58 "
       model="   0" pdb=" CZ  ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.326  1.366 -0.040 1.10e-02 8.26e+03 1.32e+01
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
       94.38 -   102.12: 10
      102.12 -   109.86: 1930
      109.86 -   117.60: 1175
      117.60 -   125.35: 928
      125.35 -   133.09: 34
  Bond angle restraints: 4077
  Sorted by residual:
  angle model="   0" pdb=" CA  PHE A  45 "
        model="   0" pdb=" CB  PHE A  45 "
        model="   0" pdb=" CG  PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.80  106.66    7.14 1.00e+00 1.00e+00 5.09e+01
  angle model="   0" pdb=" C   ASP A 110 "
        model="   0" pdb=" N   TYR A 111 "
        model="   0" pdb=" CA  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     121.70  133.09  -11.39 1.80e+00 3.09e-01 4.00e+01
  angle model="   0" pdb=" CA  TYR A 111 "
        model="   0" pdb=" CB  TYR A 111 "
        model="   0" pdb=" CG  TYR A 111 "
      ideal   model   delta    sigma   weight residual
     113.90  102.70   11.20 1.80e+00 3.09e-01 3.87e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" CB  ASP A 118 "
        model="   0" pdb=" CG  ASP A 118 "
      ideal   model   delta    sigma   weight residual
     112.60  106.88    5.72 1.00e+00 1.00e+00 3.27e+01
  angle model="   0" pdb=" CA  ASP A  23 "
        model="   0" pdb=" CB  ASP A  23 "
        model="   0" pdb=" CG  ASP A  23 "
      ideal   model   delta    sigma   weight residual
     112.60  107.06    5.54 1.00e+00 1.00e+00 3.07e+01
  ... (remaining 4072 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 958
       16.01 -    32.01: 47
       32.01 -    48.02: 14
       48.02 -    64.03: 9
       64.03 -    80.04: 4
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  50 "
           model="   0" pdb=" C   TYR A  50 "
           model="   0" pdb=" N   ILE A  51 "
           model="   0" pdb=" CA  ILE A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.96  -18.04     0      5.00e+00 4.00e-02 1.30e+01
  dihedral model="   0" pdb=" CA  GLY A  73 "
           model="   0" pdb=" C   GLY A  73 "
           model="   0" pdb=" N   ASP A  74 "
           model="   0" pdb=" CA  ASP A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.08  -16.92     0      5.00e+00 4.00e-02 1.15e+01
  dihedral model="   0" pdb=" C   THR A  34 "
           model="   0" pdb=" N   THR A  34 "
           model="   0" pdb=" CA  THR A  34 "
           model="   0" pdb=" CB  THR A  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -113.94   -8.06     0      2.50e+00 1.60e-01 1.04e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 131
       0.085 -    0.170: 29
       0.170 -    0.255: 11
       0.255 -    0.340: 3
       0.340 -    0.425: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  50 "
            model="   0" pdb=" N   TYR A  50 "
            model="   0" pdb=" C   TYR A  50 "
            model="   0" pdb=" CB  TYR A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.51e+00
  chirality model="   0" pdb=" CA  PRO A   6 "
            model="   0" pdb=" N   PRO A   6 "
            model="   0" pdb=" C   PRO A   6 "
            model="   0" pdb=" CB  PRO A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.34    0.37 2.00e-01 2.50e+01 3.51e+00
  chirality model="   0" pdb=" CA  PRO A 102 "
            model="   0" pdb=" N   PRO A 102 "
            model="   0" pdb=" C   PRO A 102 "
            model="   0" pdb=" CB  PRO A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 173 not shown)

  Planarity restraints: 326
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LYS A 113 "    0.068 5.00e-02 4.00e+02   1.04e-01 1.74e+01
        model="   0" pdb=" N   PRO A 114 "   -0.181 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A 114 "    0.058 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A 114 "    0.055 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LYS A 101 "    0.055 5.00e-02 4.00e+02   8.40e-02 1.13e+01
        model="   0" pdb=" N   PRO A 102 "   -0.145 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A 102 "    0.046 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A 102 "    0.045 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.054 5.00e-02 4.00e+02   8.30e-02 1.10e+01
        model="   0" pdb=" N   PRO A   6 "    0.144 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "   -0.046 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 323 not shown)

  Histogram of nonbonded interaction distances:
        1.22 -     1.89: 54
        1.89 -     2.57: 2402
        2.57 -     3.25: 7187
        3.25 -     3.92: 7874
        3.92 -     4.60: 12624
  Nonbonded interactions: 30141
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  78 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.218 2.270
  nonbonded model="   0" pdb="HG22 THR A  83 "
            model="   0" pdb=" H   GLU A  84 "
     model   vdw
     1.369 2.270
  nonbonded model="   0" pdb="HD11 LEU A   2 "
            model="   0" pdb=" HG  LEU A  61 "
     model   vdw
     1.426 2.440
  nonbonded model="   0" pdb="HD13 ILE A 131 "
            model="   0" pdb=" HB2 HIS A 134 "
     model   vdw
     1.554 2.440
  nonbonded model="   0" pdb=" HG2 PRO A  54 "
            model="   0" pdb="HG23 VAL A  57 "
     model   vdw
     1.562 2.440
  ... (remaining 30136 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  3.037)
  Mean delta:    0.012 (Z=  0.638)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.352 (Z=  3.903)
  Mean delta:    1.618 (Z=  0.878)

                      ----------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   158.78    21.22  5.00e+00  1.80e+01   4.2*sigma

  Min. delta:    0.018
  Max. delta:   86.853
  Mean delta:   13.184

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.208
  Mean delta:    0.077

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2241  Z= 0.454
    Angle     :  1.550   6.352   4077  Z= 0.669
    Chirality :  0.077   0.208    176
    Planarity :  0.008   0.049    326
    Dihedral  : 11.559  89.954    768
    Min Nonbonded Distance : 1.661
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  3.65 %
      Favored  : 94.89 %
    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:  0.02 (0.72), residues: 137
    helix: -0.21 (0.51), residues: 89
    sheet: -1.41 (1.71), residues: 10
    loop :  1.62 (1.19), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.022   0.005   PHE A  45 
   TYR   0.066   0.009   TYR A  50 
   ARG   0.042   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.013   0.005   PHE A  67 
   TYR   0.053   0.011   TYR A  50 
   ARG   0.002   0.000   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   1.46 %
                favored =  94.89 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.55
  MolProbity score      =   2.00

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  3.279)
  Mean delta:    0.012 (Z=  0.634)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.105 (Z=  3.691)
  Mean delta:    1.577 (Z=  0.868)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   154.23    25.77  5.00e+00  2.66e+01   5.2*sigma

  Min. delta:    0.002
  Max. delta:   80.840
  Mean delta:   12.828

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.193
  Mean delta:    0.075

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.085
  Mean delta:    0.012

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.041   2241  Z= 0.451
    Angle     :  1.529   6.119   4077  Z= 0.663
    Chirality :  0.075   0.193    176
    Planarity :  0.008   0.064    326
    Dihedral  : 11.153  80.840    768
    Min Nonbonded Distance : 1.612
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  4.84 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.12 (0.73), residues: 137
    helix:  0.00 (0.49), residues: 89
    sheet: -1.50 (1.56), residues: 10
    loop :  1.31 (1.29), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.027   0.005   PHE A  45 
   TYR   0.062   0.010   TYR A  50 
   ARG   0.070   0.014   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.017   0.005   PHE A  45 
   TYR   0.052   0.011   TYR A  50 
   ARG   0.005   0.002   ARG A 127 

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

   A  66  GLN

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

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   3.16
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.53
  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      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  3.110)
  Mean delta:    0.012 (Z=  0.626)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.54     4.06  1.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.098 (Z=  4.059)
  Mean delta:    1.571 (Z=  0.866)

                      ----------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   159.10    20.90  5.00e+00  1.75e+01   4.2*sigma

  Min. delta:    0.036
  Max. delta:   85.275
  Mean delta:   12.286

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.194
  Mean delta:    0.075

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.044
  Mean delta:    0.011

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.041   2241  Z= 0.446
    Angle     :  1.526   6.098   4077  Z= 0.662
    Chirality :  0.075   0.194    176
    Planarity :  0.008   0.044    326
    Dihedral  : 10.986  85.275    768
    Min Nonbonded Distance : 1.704
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    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 : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.01 (0.69), residues: 137
    helix: -0.16 (0.48), residues: 92
    sheet: -1.53 (1.60), residues: 10
    loop :  1.62 (1.21), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.004   PHE A  45 
   TYR   0.064   0.012   TYR A  50 
   ARG   0.036   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.010   0.004   PHE A  67 
   TYR   0.053   0.014   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.042 (Z=  3.528)
  Mean delta:    0.012 (Z=  0.637)

                        ----------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

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.580 (Z=  4.207)
  Mean delta:    1.600 (Z=  0.876)

                      ----------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   147.79    32.21  5.00e+00  4.15e+01   6.4*sigma

  Min. delta:    0.011
  Max. delta:   83.857
  Mean delta:   12.405

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.236
  Mean delta:    0.081

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.051
  Mean delta:    0.011

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.042   2241  Z= 0.454
    Angle     :  1.549   6.580   4077  Z= 0.670
    Chirality :  0.081   0.236    176
    Planarity :  0.008   0.051    326
    Dihedral  : 11.297  83.857    768
    Min Nonbonded Distance : 1.611
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    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: -0.47 (0.67), residues: 137
    helix: -0.47 (0.46), residues: 90
    sheet: -1.26 (1.55), residues: 10
    loop :  1.00 (1.16), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS A 139 
   PHE   0.019   0.004   PHE A  45 
   TYR   0.060   0.009   TYR A  50 
   ARG   0.037   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS A 139 
   PHE   0.012   0.004   PHE A  67 
   TYR   0.050   0.011   TYR A  50 
   ARG   0.002   0.001   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            =   2.71
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.53
  MolProbity score      =   1.46

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   3.16
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.55
  MolProbity score      =   1.62

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.050 (Z=  3.828)
  Mean delta:    0.019 (Z=  0.998)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90    99.59    14.31  1.80e+00  6.32e+01   7.9*sigma
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   106.45     7.35  1.00e+00  5.40e+01   7.3*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   105.49     7.11  1.00e+00  5.05e+01   7.1*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   105.82     6.78  1.00e+00  4.59e+01   6.8*sigma
   A 103  ASP  CA
   A 103  ASP  CB
   A 103  ASP  CG        112.60   106.54     6.06  1.00e+00  3.68e+01   6.1*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   132.55   -10.85  1.80e+00  3.64e+01   6.0*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   106.60     6.00  1.00e+00  3.60e+01   6.0*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   106.72     5.88  1.00e+00  3.45e+01   5.9*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   131.62    -9.92  1.80e+00  3.04e+01   5.5*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   107.20     5.40  1.00e+00  2.92e+01   5.4*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   109.00     7.90  1.50e+00  2.78e+01   5.3*sigma
   A 110  ASP  CA
   A 110  ASP  CB
   A 110  ASP  CG        112.60   107.46     5.14  1.00e+00  2.64e+01   5.1*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   130.95    -9.25  1.80e+00  2.64e+01   5.1*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   107.57     5.03  1.00e+00  2.53e+01   5.0*sigma
   A 133  GLU  CB
   A 133  GLU  CG
   A 133  GLU  CD        112.60   104.30     8.30  1.70e+00  2.39e+01   4.9*sigma
   A 136  HIS  CA
   A 136  HIS  CB
   A 136  HIS  CG        113.80   109.02     4.78  1.00e+00  2.28e+01   4.8*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.32     4.68  1.00e+00  2.19e+01   4.7*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   105.54     8.36  1.80e+00  2.16e+01   4.6*sigma
   A   7  ASP  CA
   A   7  ASP  CB
   A   7  ASP  CG        112.60   108.03     4.57  1.00e+00  2.09e+01   4.6*sigma
   A  19  LYS  C
   A  19  LYS  CA
   A  19  LYS  CB        110.10   101.43     8.67  1.90e+00  2.08e+01   4.6*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.44     4.56  1.00e+00  2.08e+01   4.6*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.45     4.55  1.00e+00  2.07e+01   4.6*sigma
   A 119  LEU  C
   A 119  LEU  CA
   A 119  LEU  CB        110.10   101.50     8.60  1.90e+00  2.05e+01   4.5*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.53     4.47  1.00e+00  2.00e+01   4.5*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.55     4.45  1.00e+00  1.98e+01   4.4*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.58     4.42  1.00e+00  1.96e+01   4.4*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.58     4.42  1.00e+00  1.95e+01   4.4*sigma
   A  52  PRO  N
   A  52  PRO  CA
   A  52  PRO  CB        103.00   107.78    -4.78  1.10e+00  1.89e+01   4.3*sigma
   A  67  PHE  CA
   A  67  PHE  CB
   A  67  PHE  CG        113.80   109.63     4.17  1.00e+00  1.74e+01   4.2*sigma
   A 135  HIS  ND1
   A 135  HIS  CE1
   A 135  HIS  NE2       108.40   112.48    -4.08  1.00e+00  1.67e+01   4.1*sigma
   A 123  GLU  CB
   A 123  GLU  CG
   A 123  GLU  CD        112.60   105.68     6.92  1.70e+00  1.66e+01   4.1*sigma
   A  89  TYR  CA
   A  89  TYR  CB
   A  89  TYR  CG        113.90   106.58     7.32  1.80e+00  1.65e+01   4.1*sigma
   A 107  LEU  C
   A 108  ILE  N
   A 108  ILE  CA        121.70   128.99    -7.29  1.80e+00  1.64e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   14.305 (Z=  7.947)
  Mean delta:    2.301 (Z=  1.353)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   88.723
  Mean delta:   13.454

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.508
  Mean delta:    0.120

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.111
  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  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.050   2241  Z= 0.710
    Angle     :  2.036  14.305   4077  Z= 0.964
    Chirality :  0.120   0.508    176
    Planarity :  0.013   0.111    326
    Dihedral  : 11.606  88.723    768
    Min Nonbonded Distance : 1.353
  
  Molprobity Statistics.
    All-atom Clashscore : 48.71
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  8.03 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  3.23 %
      Favored  : 95.97 %
    Cbeta Deviations :  2.27 %
    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: -2.18 (0.60), residues: 137
    helix:  0.20 (0.54), residues: 66
    sheet:  None (None), residues: 0
    loop : -3.25 (0.57), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 136 
   PHE   0.016   0.003   PHE A  15 
   TYR   0.021   0.003   TYR A  50 
   ARG   0.011   0.002   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 136 
   PHE   0.012   0.002   PHE A  15 
   TYR   0.016   0.003   TYR A  50 
   ARG   0.003   0.001   ARG A 127 

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

   A  72  ASN
   A 135  HIS
   A 138  HIS

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.026 (Z=  1.844)
  Mean delta:    0.005 (Z=  0.279)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    3.788 (Z=  1.930)
  Mean delta:    0.806 (Z=  0.389)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.025
  Max. delta:   89.627
  Mean delta:   10.154

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.140
  Mean delta:    0.040

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.004

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


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

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.026   2241  Z= 0.199
    Angle     :  1.126   5.324   4077  Z= 0.413
    Chirality :  0.040   0.140    176
    Planarity :  0.003   0.026    326
    Dihedral  :  9.470  89.627    768
    Min Nonbonded Distance : 1.661
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.76 (0.69), residues: 137
    helix:  1.27 (0.50), residues: 91
    sheet: -0.54 (1.57), residues: 10
    loop :  1.85 (1.11), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.004   0.001   PHE A  67 
   TYR   0.011   0.002   TYR A 105 
   ARG   0.013   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.011   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  28  GLN

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  89.78 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     3
  Clashscore            =  48.71
  RMS(bonds)            =   0.0132
  RMS(angles)           =   2.04
  MolProbity score      =   2.72

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0033
  RMS(angles)           =   1.13
  MolProbity score      =   1.35

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.035 (Z=  2.500)
  Mean delta:    0.005 (Z=  0.291)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    5.453 (Z=  1.880)
  Mean delta:    0.797 (Z=  0.381)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.014
  Max. delta:   83.989
  Mean delta:   11.438

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.125
  Mean delta:    0.039

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.035   2241  Z= 0.208
    Angle     :  1.123   5.453   4077  Z= 0.410
    Chirality :  0.039   0.125    176
    Planarity :  0.003   0.026    326
    Dihedral  : 10.877  83.989    768
    Min Nonbonded Distance : 1.591
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.81 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.27 (0.69), residues: 137
    helix:  0.80 (0.50), residues: 87
    sheet: -1.03 (1.42), residues: 10
    loop :  1.93 (1.09), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 135 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.014   0.002   TYR A 111 
   ARG   0.005   0.002   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 135 
   PHE   0.001   0.000   PHE A  67 
   TYR   0.014   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0034
  RMS(angles)           =   1.12
  MolProbity score      =   1.32

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.039 (Z=  2.819)
  Mean delta:    0.012 (Z=  0.603)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.426 (Z=  3.606)
  Mean delta:    1.555 (Z=  0.857)

                      ----------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   149.20    30.80  5.00e+00  3.79e+01   6.2*sigma

  Min. delta:    0.002
  Max. delta:   82.192
  Mean delta:   12.531

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.227
  Mean delta:    0.075

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.084
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2241  Z= 0.429
    Angle     :  1.518   6.426   4077  Z= 0.657
    Chirality :  0.075   0.227    176
    Planarity :  0.008   0.064    326
    Dihedral  : 10.914  82.192    768
    Min Nonbonded Distance : 1.606
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    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:  0.40 (0.73), residues: 137
    helix: -0.02 (0.48), residues: 89
    sheet: -0.77 (1.78), residues: 10
    loop :  1.89 (1.31), residues: 38
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 135 
   PHE   0.021   0.004   PHE A  67 
   TYR   0.059   0.010   TYR A  12 
   ARG   0.069   0.015   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 135 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.049   0.012   TYR A 111 
   ARG   0.005   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  96.35 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.52
  MolProbity score      =   1.55

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 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:    0.023 (Z=  1.625)
  Mean delta:    0.004 (Z=  0.242)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.883 (Z=  1.629)
  Mean delta:    0.863 (Z=  0.414)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   86.390
  Mean delta:   10.905

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.150
  Mean delta:    0.042

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.004

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.023   2241  Z= 0.173
    Angle     :  1.147   5.307   4077  Z= 0.424
    Chirality :  0.042   0.150    176
    Planarity :  0.003   0.026    326
    Dihedral  : 10.762  86.390    768
    Min Nonbonded Distance : 1.565
  
  Molprobity Statistics.
    All-atom Clashscore : 6.77
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.65 (0.72), residues: 137
    helix:  1.42 (0.53), residues: 92
    sheet: -1.88 (1.34), residues: 10
    loop :  1.53 (1.13), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.002   HIS A 135 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.013   0.002   TYR A 111 
   ARG   0.014   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.002   HIS A 135 
   PHE   0.002   0.001   PHE A  15 
   TYR   0.012   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 134  HIS

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.77
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.15
  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      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.050 (Z=  3.785)
  Mean delta:    0.018 (Z=  0.996)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   100.97    12.93  1.80e+00  5.16e+01   7.2*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   106.14     6.46  1.00e+00  4.18e+01   6.5*sigma
   A   7  ASP  CA
   A   7  ASP  CB
   A   7  ASP  CG        112.60   106.34     6.26  1.00e+00  3.92e+01   6.3*sigma
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   107.56     6.24  1.00e+00  3.90e+01   6.2*sigma
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        121.70   111.02    10.68  1.80e+00  3.52e+01   5.9*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   132.35   -10.65  1.80e+00  3.50e+01   5.9*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   107.28     5.32  1.00e+00  2.83e+01   5.3*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   130.64    -8.94  1.80e+00  2.47e+01   5.0*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   107.81     4.79  1.00e+00  2.29e+01   4.8*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   129.98    -8.28  1.80e+00  2.12e+01   4.6*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   108.02     4.58  1.00e+00  2.10e+01   4.6*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   108.02     4.58  1.00e+00  2.10e+01   4.6*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.49     4.51  1.00e+00  2.04e+01   4.5*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.50     4.50  1.00e+00  2.03e+01   4.5*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.50     4.50  1.00e+00  2.03e+01   4.5*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.54     4.46  1.00e+00  1.99e+01   4.5*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   108.14     4.46  1.00e+00  1.99e+01   4.5*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.57     4.43  1.00e+00  1.96e+01   4.4*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.60     4.40  1.00e+00  1.94e+01   4.4*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.60     4.40  1.00e+00  1.93e+01   4.4*sigma
   A  15  PHE  CA
   A  15  PHE  CB
   A  15  PHE  CG        113.80   109.42     4.38  1.00e+00  1.92e+01   4.4*sigma
   A 107  LEU  C
   A 108  ILE  N
   A 108  ILE  CA        121.70   129.34    -7.64  1.80e+00  1.80e+01   4.2*sigma
   A 110  ASP  CA
   A 110  ASP  CB
   A 110  ASP  CG        112.60   108.42     4.18  1.00e+00  1.74e+01   4.2*sigma
   A  75  GLU  C
   A  76  SER  N
   A  76  SER  CA        121.70   129.18    -7.48  1.80e+00  1.73e+01   4.2*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   129.18    -7.48  1.80e+00  1.73e+01   4.2*sigma
   A 103  ASP  C
   A 104  VAL  N
   A 104  VAL  CA        121.70   129.07    -7.37  1.80e+00  1.68e+01   4.1*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   110.78     6.12  1.50e+00  1.66e+01   4.1*sigma
   A  50  TYR  CA
   A  50  TYR  C
   A  51  ILE  N         116.20   124.31    -8.11  2.00e+00  1.64e+01   4.1*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   102.43     7.67  1.90e+00  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   12.925 (Z=  7.181)
  Mean delta:    2.276 (Z=  1.320)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   71.979
  Mean delta:   12.608

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.518
  Mean delta:    0.112

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.089
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.050   2241  Z= 0.709
    Angle     :  2.036  12.925   4077  Z= 0.949
    Chirality :  0.112   0.518    176
    Planarity :  0.010   0.089    326
    Dihedral  : 11.301  71.979    768
    Min Nonbonded Distance : 1.114
  
  Molprobity Statistics.
    All-atom Clashscore : 74.88
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  : 10.22 %
      Favored  : 87.59 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  8.06 %
      Favored  : 87.10 %
    Cbeta Deviations :  0.76 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.40 (0.57), residues: 137
    helix: -0.16 (0.54), residues: 60
    sheet:  None (None), residues: 0
    loop : -2.96 (0.54), residues: 77
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 138 
   PHE   0.007   0.001   PHE A  15 
   TYR   0.017   0.003   TYR A  50 
   ARG   0.026   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 138 
   PHE   0.005   0.001   PHE A  15 
   TYR   0.012   0.002   TYR A  50 
   ARG   0.002   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 135  HIS

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  87.59 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     1
  Clashscore            =  74.88
  RMS(bonds)            =   0.0131
  RMS(angles)           =   2.04
  MolProbity score      =   3.47

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.053 (Z=  3.679)
  Mean delta:    0.019 (Z=  0.996)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   105.91     7.89  1.00e+00  6.23e+01   7.9*sigma
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   101.41    12.49  1.80e+00  4.82e+01   6.9*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   106.06     6.54  1.00e+00  4.28e+01   6.5*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   132.68   -10.98  1.80e+00  3.72e+01   6.1*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   106.59     6.01  1.00e+00  3.61e+01   6.0*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   106.99     5.61  1.00e+00  3.15e+01   5.6*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   108.60     8.30  1.50e+00  3.06e+01   5.5*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   130.81    -9.11  1.80e+00  2.56e+01   5.1*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   107.58     5.02  1.00e+00  2.52e+01   5.0*sigma
   A   3  LEU  C
   A   4  ILE  N
   A   4  ILE  CA        121.70   130.57    -8.87  1.80e+00  2.43e+01   4.9*sigma
   A 110  ASP  CA
   A 110  ASP  CB
   A 110  ASP  CG        112.60   107.68     4.92  1.00e+00  2.42e+01   4.9*sigma
   A  29  ASP  CA
   A  29  ASP  CB
   A  29  ASP  CG        112.60   107.96     4.64  1.00e+00  2.16e+01   4.6*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   108.01     4.59  1.00e+00  2.11e+01   4.6*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.42     4.58  1.00e+00  2.09e+01   4.6*sigma
   A  93  LEU  C
   A  93  LEU  CA
   A  93  LEU  CB        110.10   101.52     8.58  1.90e+00  2.04e+01   4.5*sigma
   A  44  ASP  CA
   A  44  ASP  CB
   A  44  ASP  CG        112.60   108.12     4.48  1.00e+00  2.00e+01   4.5*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   108.14     4.46  1.00e+00  1.99e+01   4.5*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.55     4.45  1.00e+00  1.98e+01   4.5*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.57     4.43  1.00e+00  1.96e+01   4.4*sigma
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        121.70   129.59    -7.89  1.80e+00  1.92e+01   4.4*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.62     4.38  1.00e+00  1.92e+01   4.4*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.62     4.38  1.00e+00  1.92e+01   4.4*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.65     4.35  1.00e+00  1.90e+01   4.4*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   106.12     7.78  1.80e+00  1.87e+01   4.3*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.70     4.30  1.00e+00  1.85e+01   4.3*sigma
   A  24  GLU  CB
   A  24  GLU  CG
   A  24  GLU  CD        112.60   105.33     7.27  1.70e+00  1.83e+01   4.3*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   129.26    -7.56  1.80e+00  1.77e+01   4.2*sigma
   A   7  ASP  CA
   A   7  ASP  CB
   A   7  ASP  CG        112.60   108.47     4.13  1.00e+00  1.70e+01   4.1*sigma
   A 107  LEU  C
   A 108  ILE  N
   A 108  ILE  CA        121.70   129.10    -7.40  1.80e+00  1.69e+01   4.1*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   129.09    -7.39  1.80e+00  1.69e+01   4.1*sigma
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        121.70   129.08    -7.38  1.80e+00  1.68e+01   4.1*sigma
   A  77  ILE  C
   A  77  ILE  CA
   A  77  ILE  CB        111.60   103.40     8.20  2.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   12.494 (Z=  7.892)
  Mean delta:    2.273 (Z=  1.328)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.007
  Max. delta:   89.608
  Mean delta:   12.697

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.471
  Mean delta:    0.098

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.083
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.053   2241  Z= 0.709
    Angle     :  2.031  12.494   4077  Z= 0.952
    Chirality :  0.098   0.471    176
    Planarity :  0.010   0.083    326
    Dihedral  : 11.667  89.608    768
    Min Nonbonded Distance : 1.122
  
  Molprobity Statistics.
    All-atom Clashscore : 69.01
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  : 10.22 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.84 %
      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: -2.34 (0.60), residues: 137
    helix:  0.14 (0.56), residues: 66
    sheet:  None (None), residues: 0
    loop : -3.43 (0.55), residues: 71
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 135 
   PHE   0.007   0.002   PHE A  15 
   TYR   0.020   0.003   TYR A  50 
   ARG   0.013   0.002   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 135 
   PHE   0.005   0.001   PHE A  15 
   TYR   0.015   0.003   TYR A  50 
   ARG   0.001   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN
   A 134  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.056 (Z=  3.700)
  Mean delta:    0.019 (Z=  1.001)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        121.70   137.61   -15.91  1.80e+00  7.81e+01   8.8*sigma
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   100.61    13.29  1.80e+00  5.45e+01   7.4*sigma
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   107.03     6.77  1.00e+00  4.58e+01   6.8*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   106.28     6.32  1.00e+00  4.00e+01   6.3*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   132.49   -10.79  1.80e+00  3.59e+01   6.0*sigma
   A  15  PHE  CA
   A  15  PHE  CB
   A  15  PHE  CG        113.80   108.57     5.23  1.00e+00  2.74e+01   5.2*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   131.10    -9.40  1.80e+00  2.72e+01   5.2*sigma
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        121.70   131.06    -9.36  1.80e+00  2.70e+01   5.2*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   107.46     5.14  1.00e+00  2.64e+01   5.1*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   107.65     4.95  1.00e+00  2.45e+01   4.9*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   107.88     4.72  1.00e+00  2.23e+01   4.7*sigma
   A   7  ASP  CA
   A   7  ASP  CB
   A   7  ASP  CG        112.60   108.05     4.55  1.00e+00  2.07e+01   4.6*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   129.80    -8.10  1.80e+00  2.03e+01   4.5*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.54     4.46  1.00e+00  1.99e+01   4.5*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.55     4.45  1.00e+00  1.98e+01   4.5*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.56     4.44  1.00e+00  1.97e+01   4.4*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.61     4.39  1.00e+00  1.93e+01   4.4*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.61     4.39  1.00e+00  1.93e+01   4.4*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.63     4.37  1.00e+00  1.91e+01   4.4*sigma
   A  70  LEU  C
   A  70  LEU  CA
   A  70  LEU  CB        110.10   101.86     8.24  1.90e+00  1.88e+01   4.3*sigma
   A  41  VAL  C
   A  41  VAL  CA
   A  41  VAL  CB        111.40   103.18     8.22  1.90e+00  1.87e+01   4.3*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.69     4.31  1.00e+00  1.86e+01   4.3*sigma
   A  78  ILE  C
   A  79  LYS  N
   A  79  LYS  CA        121.70   129.38    -7.68  1.80e+00  1.82e+01   4.3*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   108.34     4.26  1.00e+00  1.82e+01   4.3*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   129.30    -7.60  1.80e+00  1.78e+01   4.2*sigma
   A   2  LEU  C
   A   3  LEU  N
   A   3  LEU  CA        121.70   129.24    -7.54  1.80e+00  1.75e+01   4.2*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   110.68     6.22  1.50e+00  1.72e+01   4.1*sigma
   A 110  ASP  CA
   A 110  ASP  CB
   A 110  ASP  CG        112.60   108.49     4.11  1.00e+00  1.69e+01   4.1*sigma
   A   2  LEU  N
   A   2  LEU  CA
   A   2  LEU  CB        110.50   117.43    -6.93  1.70e+00  1.66e+01   4.1*sigma
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        121.70   128.93    -7.23  1.80e+00  1.61e+01   4.0*sigma
   A  75  GLU  CB
   A  75  GLU  CG
   A  75  GLU  CD        112.60   105.77     6.83  1.70e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   15.908 (Z=  8.838)
  Mean delta:    2.329 (Z=  1.343)

                      ----------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  -148.48   -31.52  5.00e+00  3.98e+01   6.3*sigma

  Min. delta:    0.001
  Max. delta:   59.259
  Mean delta:   11.761

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.447
  Mean delta:    0.111

                       ----------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  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.056   2241  Z= 0.713
    Angle     :  2.076  15.908   4077  Z= 0.966
    Chirality :  0.111   0.447    176
    Planarity :  0.012   0.099    326
    Dihedral  : 10.607  60.054    768
    Min Nonbonded Distance : 1.111
  
  Molprobity Statistics.
    All-atom Clashscore : 70.37
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  9.49 %
      Favored  : 89.05 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  4.03 %
      Favored  : 91.94 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.40 (0.60), residues: 137
    helix:  0.32 (0.60), residues: 59
    sheet:  None (None), residues: 0
    loop : -3.37 (0.52), residues: 78
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.007   0.002   PHE A  67 
   TYR   0.020   0.004   TYR A  50 
   ARG   0.041   0.007   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.017   0.003   TYR A  50 
   ARG   0.006   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN
   A 135  HIS

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  88.32 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  69.01
  RMS(bonds)            =   0.0132
  RMS(angles)           =   2.03
  MolProbity score      =   3.06

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.024 (Z=  1.724)
  Mean delta:    0.004 (Z=  0.255)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.684 (Z=  1.510)
  Mean delta:    0.806 (Z=  0.387)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   86.366
  Mean delta:   10.537

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.131
  Mean delta:    0.039

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.004

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.024   2241  Z= 0.182
    Angle     :  1.125   5.470   4077  Z= 0.412
    Chirality :  0.039   0.131    176
    Planarity :  0.003   0.026    326
    Dihedral  :  9.707  86.366    768
    Min Nonbonded Distance : 1.083
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    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:  2.39 (0.71), residues: 137
    helix:  1.81 (0.52), residues: 86
    sheet: -0.37 (1.86), residues: 10
    loop :  1.94 (1.08), residues: 41
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.005   0.001   PHE A  15 
   TYR   0.015   0.002   TYR A 111 
   ARG   0.014   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.004   0.001   PHE A  67 
   TYR   0.013   0.002   TYR A 111 
   ARG   0.002   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      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.028 (Z=  2.030)
  Mean delta:    0.006 (Z=  0.356)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.630 (Z=  1.545)
  Mean delta:    0.835 (Z=  0.394)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.015
  Max. delta:   87.092
  Mean delta:   12.125

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.123
  Mean delta:    0.043

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.004

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.004   0.028   2241  Z= 0.254
    Angle     :  1.139   5.569   4077  Z= 0.416
    Chirality :  0.043   0.123    176
    Planarity :  0.003   0.026    326
    Dihedral  : 11.003  87.092    768
    Min Nonbonded Distance : 1.475
  
  Molprobity Statistics.
    All-atom Clashscore : 7.22
    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:  2.00 (0.72), residues: 137
    helix:  1.49 (0.51), residues: 90
    sheet: -0.16 (1.72), residues: 10
    loop :  1.70 (1.18), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.013   0.002   TYR A 111 
   ARG   0.014   0.003   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.012   0.002   TYR A 111 
   ARG   0.003   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  89.05 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =  70.37
  RMS(bonds)            =   0.0132
  RMS(angles)           =   2.08
  MolProbity score      =   3.35

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            =   8.12
  RMS(bonds)            =   0.0031
  RMS(angles)           =   1.12
  MolProbity score      =   1.44

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            =   7.22
  RMS(bonds)            =   0.0041
  RMS(angles)           =   1.14
  MolProbity score      =   1.40

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.025 (Z=  1.753)
  Mean delta:    0.005 (Z=  0.303)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.411 (Z=  2.290)
  Mean delta:    0.974 (Z=  0.434)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   83.595
  Mean delta:   11.467

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.249
  Mean delta:    0.071

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.031
  Mean delta:    0.004

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.004   0.025   2241  Z= 0.216
    Angle     :  1.244   6.411   4077  Z= 0.451
    Chirality :  0.071   0.249    176
    Planarity :  0.003   0.031    326
    Dihedral  : 11.031  83.595    768
    Min Nonbonded Distance : 1.482
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 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:  0.40 (0.69), residues: 137
    helix:  0.13 (0.55), residues: 80
    sheet: -0.64 (1.53), residues: 10
    loop :  1.14 (0.92), residues: 47
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 138 
   PHE   0.017   0.003   PHE A  67 
   TYR   0.052   0.007   TYR A 111 
   ARG   0.007   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 138 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.044   0.008   TYR A 111 
   ARG   0.002   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0038
  RMS(angles)           =   1.24
  MolProbity score      =   1.45

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.911)
  Mean delta:    0.012 (Z=  0.613)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.602 (Z=  3.940)
  Mean delta:    1.586 (Z=  0.873)

                      ----------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   145.14    34.86  5.00e+00  4.86e+01   7.0*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   152.38    27.62  5.00e+00  3.05e+01   5.5*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   153.58    26.42  5.00e+00  2.79e+01   5.3*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   155.41    24.59  5.00e+00  2.42e+01   4.9*sigma

  Min. delta:    0.023
  Max. delta:   84.864
  Mean delta:   12.874

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.189
  Mean delta:    0.074

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.106
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2241  Z= 0.437
    Angle     :  1.528   7.602   4077  Z= 0.664
    Chirality :  0.074   0.189    176
    Planarity :  0.009   0.079    326
    Dihedral  : 10.998  84.864    768
    Min Nonbonded Distance : 1.610
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  7.30 %
      Favored  : 91.97 %
    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 : 0.76 %
  
  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: -0.01 (0.72), residues: 137
    helix:  0.23 (0.50), residues: 90
    sheet: -1.56 (1.76), residues: 10
    loop :  0.32 (1.23), residues: 37
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A  43 
   PHE   0.018   0.004   PHE A  45 
   TYR   0.064   0.010   TYR A  50 
   ARG   0.083   0.015   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A  43 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.051   0.012   TYR A  50 
   ARG   0.010   0.002   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  91.97 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.53
  MolProbity score      =   1.84

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.023 (Z=  1.636)
  Mean delta:    0.004 (Z=  0.253)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    5.087 (Z=  2.826)
  Mean delta:    0.861 (Z=  0.415)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   88.081
  Mean delta:   12.302

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.192
  Mean delta:    0.042

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.026
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.023   2241  Z= 0.180
    Angle     :  1.147   6.279   4077  Z= 0.424
    Chirality :  0.042   0.192    176
    Planarity :  0.003   0.026    326
    Dihedral  : 11.078  88.081    768
    Min Nonbonded Distance : 1.603
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    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:  2.17 (0.71), residues: 137
    helix:  1.30 (0.52), residues: 91
    sheet: -0.88 (1.58), residues: 10
    loop :  3.08 (1.10), residues: 36
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.017   0.002   TYR A 111 
   ARG   0.013   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.001   0.001   PHE A  15 
   TYR   0.017   0.003   TYR A 111 
   ARG   0.002   0.001   ARG A 127 

                     ----------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            =   4.96
  RMS(bonds)            =   0.0031
  RMS(angles)           =   1.15
  MolProbity score      =   1.26

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.047 (Z=  3.679)
  Mean delta:    0.018 (Z=  0.987)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   106.76     7.04  1.00e+00  4.96e+01   7.0*sigma
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   101.67    12.23  1.80e+00  4.62e+01   6.8*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   133.19   -11.49  1.80e+00  4.08e+01   6.4*sigma
   A   7  ASP  CA
   A   7  ASP  CB
   A   7  ASP  CG        112.60   106.80     5.80  1.00e+00  3.37e+01   5.8*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   106.87     5.73  1.00e+00  3.29e+01   5.7*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   106.97     5.63  1.00e+00  3.17e+01   5.6*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   131.78   -10.08  1.80e+00  3.13e+01   5.6*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   107.31     5.29  1.00e+00  2.80e+01   5.3*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   107.73     4.87  1.00e+00  2.38e+01   4.9*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   109.89     7.01  1.50e+00  2.18e+01   4.7*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.38     4.62  1.00e+00  2.13e+01   4.6*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   107.99     4.61  1.00e+00  2.13e+01   4.6*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.51     4.49  1.00e+00  2.02e+01   4.5*sigma
   A  29  ASP  CA
   A  29  ASP  CB
   A  29  ASP  CG        112.60   108.11     4.49  1.00e+00  2.02e+01   4.5*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.52     4.48  1.00e+00  2.00e+01   4.5*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.52     4.48  1.00e+00  2.00e+01   4.5*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.56     4.44  1.00e+00  1.97e+01   4.4*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   129.64    -7.94  1.80e+00  1.95e+01   4.4*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.62     4.38  1.00e+00  1.92e+01   4.4*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.66     4.34  1.00e+00  1.89e+01   4.3*sigma
   A  50  TYR  CA
   A  50  TYR  C
   A  51  ILE  N         116.20   124.45    -8.25  2.00e+00  1.70e+01   4.1*sigma
   A 110  ASP  CA
   A 110  ASP  CB
   A 110  ASP  CG        112.60   108.52     4.08  1.00e+00  1.67e+01   4.1*sigma
   A 133  GLU  CB
   A 133  GLU  CG
   A 133  GLU  CD        112.60   105.68     6.92  1.70e+00  1.66e+01   4.1*sigma
   A 138  HIS  ND1
   A 138  HIS  CE1
   A 138  HIS  NE2       108.40   112.43    -4.03  1.00e+00  1.62e+01   4.0*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   128.95    -7.25  1.80e+00  1.62e+01   4.0*sigma
   A 103  ASP  C
   A 104  VAL  N
   A 104  VAL  CA        121.70   128.94    -7.24  1.80e+00  1.62e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   12.232 (Z=  7.043)
  Mean delta:    2.203 (Z=  1.275)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   80.887
  Mean delta:   12.094

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.494
  Mean delta:    0.104

                       ----------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  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.047   2241  Z= 0.702
    Angle     :  1.983  12.232   4077  Z= 0.920
    Chirality :  0.104   0.494    176
    Planarity :  0.013   0.099    326
    Dihedral  : 11.029  80.887    768
    Min Nonbonded Distance : 1.310
  
  Molprobity Statistics.
    All-atom Clashscore : 67.21
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  7.30 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  7.26 %
      Favored  : 87.90 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.74 (0.60), residues: 137
    helix:  0.40 (0.54), residues: 65
    sheet:  None (None), residues: 0
    loop : -2.79 (0.59), residues: 72
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 135 
   PHE   0.012   0.002   PHE A  15 
   TYR   0.020   0.002   TYR A  50 
   ARG   0.021   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 135 
   PHE   0.009   0.002   PHE A  15 
   TYR   0.016   0.002   TYR A  50 
   ARG   0.006   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 139  HIS
   A 134  HIS

=================================== Summary ===================================

  Ramachandran outliers =   2.92 %
                favored =  89.78 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     0
  Clashscore            =  67.21
  RMS(bonds)            =   0.0130
  RMS(angles)           =   1.98
  MolProbity score      =   3.37

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.055 (Z=  3.785)
  Mean delta:    0.018 (Z=  0.994)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  45  PHE  CA
   A  45  PHE  CB
   A  45  PHE  CG        113.80   106.66     7.14  1.00e+00  5.09e+01   7.1*sigma
   A 110  ASP  C
   A 111  TYR  N
   A 111  TYR  CA        121.70   133.09   -11.39  1.80e+00  4.00e+01   6.3*sigma
   A 111  TYR  CA
   A 111  TYR  CB
   A 111  TYR  CG        113.90   102.70    11.20  1.80e+00  3.87e+01   6.2*sigma
   A 118  ASP  CA
   A 118  ASP  CB
   A 118  ASP  CG        112.60   106.88     5.72  1.00e+00  3.27e+01   5.7*sigma
   A  23  ASP  CA
   A  23  ASP  CB
   A  23  ASP  CG        112.60   107.06     5.54  1.00e+00  3.07e+01   5.5*sigma
   A  49  GLU  C
   A  50  TYR  N
   A  50  TYR  CA        121.70   131.53    -9.83  1.80e+00  2.98e+01   5.5*sigma
   A 116  ASP  CA
   A 116  ASP  CB
   A 116  ASP  CG        112.60   107.23     5.37  1.00e+00  2.89e+01   5.4*sigma
   A  88  ASP  CA
   A  88  ASP  CB
   A  88  ASP  CG        112.60   107.43     5.17  1.00e+00  2.67e+01   5.2*sigma
   A 116  ASP  CA
   A 116  ASP  C
   A 117  PRO  N         116.90   109.24     7.66  1.50e+00  2.61e+01   5.1*sigma
   A  81  TYR  CA
   A  81  TYR  CB
   A  81  TYR  CG        113.90   105.39     8.51  1.80e+00  2.24e+01   4.7*sigma
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   107.87     4.73  1.00e+00  2.23e+01   4.7*sigma
   A  72  ASN  C
   A  73  GLY  N
   A  73  GLY  CA        121.70   130.07    -8.37  1.80e+00  2.16e+01   4.7*sigma
   A 134  HIS  CD2
   A 134  HIS  NE2
   A 134  HIS  CE1       109.00   104.43     4.57  1.00e+00  2.09e+01   4.6*sigma
   A  47  ASP  CA
   A  47  ASP  CB
   A  47  ASP  CG        112.60   108.08     4.52  1.00e+00  2.04e+01   4.5*sigma
   A  72  ASN  CA
   A  72  ASN  CB
   A  72  ASN  CG        112.60   108.09     4.51  1.00e+00  2.03e+01   4.5*sigma
   A 139  HIS  CD2
   A 139  HIS  NE2
   A 139  HIS  CE1       109.00   104.51     4.49  1.00e+00  2.02e+01   4.5*sigma
   A 136  HIS  CD2
   A 136  HIS  NE2
   A 136  HIS  CE1       109.00   104.54     4.46  1.00e+00  1.99e+01   4.5*sigma
   A 137  HIS  CD2
   A 137  HIS  NE2
   A 137  HIS  CE1       109.00   104.55     4.45  1.00e+00  1.98e+01   4.4*sigma
   A 135  HIS  CD2
   A 135  HIS  NE2
   A 135  HIS  CE1       109.00   104.56     4.44  1.00e+00  1.97e+01   4.4*sigma
   A 138  HIS  CD2
   A 138  HIS  NE2
   A 138  HIS  CE1       109.00   104.59     4.41  1.00e+00  1.95e+01   4.4*sigma
   A  43  HIS  CD2
   A  43  HIS  NE2
   A  43  HIS  CE1       109.00   104.62     4.38  1.00e+00  1.92e+01   4.4*sigma
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        121.70   129.58    -7.88  1.80e+00  1.92e+01   4.4*sigma
   A  15  PHE  CA
   A  15  PHE  CB
   A  15  PHE  CG        113.80   109.47     4.33  1.00e+00  1.87e+01   4.3*sigma
   A  41  VAL  C
   A  41  VAL  CA
   A  41  VAL  CB        111.40   103.61     7.79  1.90e+00  1.68e+01   4.1*sigma
   A  74  ASP  CA
   A  74  ASP  CB
   A  74  ASP  CG        112.60   108.53     4.07  1.00e+00  1.66e+01   4.1*sigma
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        121.70   128.91    -7.21  1.80e+00  1.61e+01   4.0*sigma
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   108.59     4.01  1.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:   11.388 (Z=  7.138)
  Mean delta:    2.224 (Z=  1.288)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   70.161
  Mean delta:   12.598

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.425
  Mean delta:    0.098

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.104
  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  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.013   0.055   2241  Z= 0.707
    Angle     :  1.991  11.388   4077  Z= 0.927
    Chirality :  0.098   0.425    176
    Planarity :  0.013   0.104    326
    Dihedral  : 11.974  80.036    768
    Min Nonbonded Distance : 1.218
  
  Molprobity Statistics.
    All-atom Clashscore : 66.31
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  8.03 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.84 %
      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: -2.26 (0.61), residues: 137
    helix:  0.20 (0.55), residues: 69
    sheet:  None (None), residues: 0
    loop : -3.53 (0.55), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.008   0.002   PHE A  15 
   TYR   0.019   0.003   TYR A  50 
   ARG   0.013   0.004   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.007   0.002   PHE A  15 
   TYR   0.013   0.003   TYR A  50 
   ARG   0.007   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 139  HIS
   A  72  ASN
   A 100  GLN

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  89.78 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  66.31
  RMS(bonds)            =   0.0131
  RMS(angles)           =   1.99
  MolProbity score      =   3.01

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
